Currently, there isn't an option to merge a company file in QuickBooks Online.
However, you can condense your company file if you're using a QuickBooks Desktop version. Please know that condensing your company file is irreversible. Thus said, you'll have to create a backup copy of your data first.
Once done, here's how you can condense your company file in QuickBooks Desktop:
Go to File.
Choose Condense Data.
Click Begin Condense.
This way, you can now successfully condense your large QuickBooks file. In addition, I've also included our detailed guide in condensing a company file.