Steps for batch merging PDFs

Explain how to merge several PDFs in order and save them to the original folder. It includes the preparation before merging, the merging steps of OmniDoc desktop client, the method of merging the entire folder at one time using common scripts or command line tools, and the result verification method.

Key points of this article

  • Unify the file name numbers before merging, such as 01, 02, 03, otherwise 10 will be ranked before 2, and the merge order will be wrong.
  • Several documents can be merged one by one in the PDF editor, and adjustments can be made while viewing, making it easy to find errors.
  • When merging entire folders in batches, do not place the output file in the folder being read, otherwise it will be merged again the next time it is run.
  • After merging, check whether the total number of pages is equal to the sum of the number of pages in each document, and check the dividing page of each document.
  • Back up the original files before merging, and change the output file to a new file name to avoid overwriting the original files.

Many people encounter a situation where the data of a project is split into dozens of PDF, each of which is a chapter or a week's record, and finally a complete document is synthesized, and the result is still in the original folder. This and having only three or four documents on hand and dragging them in one by one are two kinds of tasks. As soon as there are many files, the problems of order, duplicate name and overwriting the original will arise together.

This article is for readers who need to merge PDF in bulk and don't want to mess up the original. After reading, you can decide which approach to use, know what to prepare before the merger, and master the steps of merging several files with the OmniDoc desktop client. For an one-time merge of entire folders, this article talks about general practices, including how to name and how to avoid repeated merging of output files.

To be clear, this article only treats the merge steps in the PDF editor as operations that can be done directly. The part of automatic batch merge by folder is about the general idea of not relying on a specific software.

How to merge PDFs in batches without making them messy? One sentence conclusion: If there are few files, merge them one by one in the editor. If there are many files, name them uniformly and then process them all at once.

The number of files and whether repeated operations are required determine the trouble-free approach. The table below can help you compare your situation.

Your situation.Recommended practiceReason
2 to 5 documents, which need to be determined manuallyJoin the merge one by one in the PDF editor and export to the original folderYou can adjust while watching, and the errors at the boundary are easy to find.
A whole folder with a uniform number for the file nameMerge once by file name order with a script or command line toolThe order is determined by the file name and does not have to be selected one by one.
There are a lot of files, and they are done once a week.Write a fixed merge script and output it to a separate subfolderIt can be run repeatedly, and the results are consistent each time, so it is easy to review.
There are scanned documents mixed in the folderFirst use the OCR of the PDF editor to process the scanned parts, and then mergeThe merged text can be selected, and it is more convenient to retrieve and check it later.
The merge results need to be saved in the original folderRename the output file and back up the original before mergingAvoid overwriting the original file and you can start over if you make a mistake

# before you start: confirm these points first

Take a few minutes to prepare before you start, and there will be much less rework later.

- confirm the order of files. the page order of the merge result is the order in which the files are read. If the file name is Chapter 1, Chapter 10, and Chapter 2, sorting directly by name puts Chapter 10 before Chapter 2. It is suggested that the prefix "01 _" and "02 _" should be changed to the same number of digits before the sorting result is correct. - distinguish between text version and scanned parts. text version PDF can directly select text. The scanned piece is just a picture, and the text cannot be selected after the merge. If you are not sure, you can open the file and try to select a paragraph of text with the mouse: if you choose it, it will be the text version, but most of it will be scanned. Scanned pieces can be OCR first and then merged. - check whether the file can be opened properly. if a PDF has an open password, the merge tool must be able to open it with that password, otherwise it will fail halfway. When you need a password, get it from the file provider instead of looking for ways to bypass it. - back up the original. make a copy of the entire folder elsewhere before you start the operation. There is a misoperation during the merge process, and the backup can be restored directly. - Planning output location and file name. the name of the output file is different from that of any input file. For example, the input is "01_xx.pdf" to "30_xx.pdf", and the output can be called "merge result _ 2024.pdf" and saved in the original folder.

# steps to merge several PDF copies in OmniDoc Desktop client

This section is suitable for several files and is completed in the PDF editor of the desktop client.

  1. Open the download.omnidoc.top download desktop client, which supports Windows, macOS and Linux, and follow the prompts to install.

two. Open the PDF editor in the client and load the file you want to start with.

  1. Use the merge feature in the page operation to add the rest of the PDF in order.
  2. Check the merged page order. If a file is not in the right location, use the reorder function to adjust the page order.
  3. Go through the boundary one by one and make sure that the last page of each document and the first page of the next document are not misplaced or omitted.
  4. Export to PDF. In the Save dialog box, select the folder where the original file is located, and enter a new file name.
  5. Open the exported file and check the number of pages and contents as described in the next section.

# General practice of batch merging of whole folders

When there are dozens or more PDF in the folder, adding them one by one can be time-consuming and easy to miss. At this point, you can use a script or command-line tool to read and merge at one time in the order of file names. Specific tools can be selected according to your own computer environment, and here are the general steps for not relying on a particular software.

- put the files to be merged into a dedicated subfolder. put only the PDF that needs to be merged, and do not mix with the previous merge results or irrelevant files. - uniform file name prefix and number. use a number with the same number of digits as "01 _" and "02 _" to make the sorting results consistent with the order you want. - read and append pages in the order of file names. A script or command-line tool writes the pages of each file to the same output file in order. - output files should be excluded from the input. if the output file is saved in the folder being read, it will be merged as input again the next time it is run, and the number of pages will multiply. It is safe to output to another folder, or skip the name of the output file itself in the script. - first test run with two or three small documents. make sure the page order, number of pages, and boundaries are correct, and then process the entire folder.

# check item by item after completion

After you get the result of the merger, don't file it directly, check it item by item according to the table below.

Check itemWhat do you think?What if there's a problem?
Total pagesAdd up the pages of each original document and compare it with the number of pages of the merged documentIf the number of pages is reduced, check to see if any files have not been added; if there are more pages, check whether the output files have been repeatedly merged.
Page orderTurn to the front page of each document in orderRearrange the pages, or correct the file name number and remerge
DemarcationLook at the handover page between every two documentsIf there is any dislocation, go back to the original file and confirm whether there are missing pages or multiple pages.
Scanned textTry to select a paragraph of textOCR the scanned parts first, and then export them again.
Is the original in good condition?Compare the originals in the backup folderIf the original is changed, restore it with backup and re-operate it.
Page orientation and sizeScroll through to see if there is a mix of horizontal and vertical lines or sudden changes in sizeIt is normal that the size of the original file itself is different. If you need to unify, check whether there are any pages that affect your reading.

When checking, it is recommended that the scope of spot checks be placed on the first page, the last page and an intermediate page of each document. In this way, we can find not only the page order problem, but also the missing content. It is still safer to check page by page when it comes to important materials.

# Summary

The key to batch merging PDF is to sort out the file names in order before merging, back up the original, and check according to the number of pages and boundaries after merging. When there are few files, you can add them one by one in the PDF editor; when there are many folders, use a unified name plus a general script to deal with them all at once, and be careful that the output files are not repeatedly merged.

# frequently asked questions (FAQ)

1. Can scanned PDF be merged in batches?

It can be merged. The scanned piece is still a picture after merging, and the text cannot be selected. If you need to retrieve or copy the content later, use the OCR of the PDF editor to process it before merging.

2. Will the original bookmarks and catalogs be retained after the merger?

Different merge methods deal with bookmarks in different ways, some will be retained, some will be lost. After the merge is complete, open the export file and check that the directory and bookmark are still there. If you lose it, you can only supplement it manually or sort out the catalogue information of each chapter before merging.

3. What if the file names are sorted in the wrong order?

For the most part, the number of digits is inconsistent, such as "2" and "10". Add all the numbers to the same number of digits, such as "02" and "10", and then reorder them. After the file name has been changed, merge it again.

4. What should I do if the merged file is too large?

The file size mainly depends on the pictures and fonts in the original file. Before merging, you can check which files are particularly large and confirm whether these pictures are necessary. If you just need to send, you can first check the content locally, and then choose the appropriate compression method, but be aware that compression may affect the clarity of the picture.

5. Is it safe to merge files with online conversion sites?

Before uploading a file to any online website, read the privacy instructions to see if the file will be saved and used for other purposes. For documents involving contracts, medical records and undisclosed materials, it is recommended to give priority to the use of local tools.

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Updated 2026-11-12