I have a lot of books in my iBooks Library. They are not purchased from iBooks Store so it is impossible to do it automatically via iCloud. What should I do? Some backup? How? Maybe should I copy one file and then move it from one computer to another. Is there any way?
Recursively copy the contents of
from your old mac to a destination folder your new mac. Then open iBooks on your new mac. Click File->Add to Library, navigate to the destination folder you chose, and select all the files (books) you wish to import.
I couldn't figure out where exactly iBooks stores imported books but I found out something else that might help you.
Select all books you want to backup and then drag them out of iBooks onto a Finder window and they sould be copied over.
I am not sure but it seems unlikely, that your reading progress and/or bookmarks are being copied as well. If you don't mind that, than this would do the trick.
Otherwise someone else might be able to locate the folder where iBooks stores the books. I found this answer to that question but on my Mac it didn't seem to be correct: Link