iExplorer makes it really easy to access and transfer any of your iBooks data from any iPhone, iPad, or iPod to your Mac or Windows PC.
TRANSFER BOOKS AND PDFs TO YOUR COMPUTER
iExplorer has a dedicated section for Books. Just click on it in the left panel, and you'll see all of your iBooks files listed in the main iExplorer window. You can simply drag/drop any of your EPUB folders (books) or PDF files to a folder on your computer or right-click and choose Export to folder. To select more than one, hold Command (Mac) or Control (PC).
Once they are on your computer, you can add them to your iTunes library by clicking on iTunes File menu Add to Library. Or, if you use Mac OS 10.9 Mavericks or 10.10 Yosemite, there is now a standalone iBooks application, so you'll import to the iBooks app instead by using iBooks File menu Add to Library.
TRANSFER BOOKS AND PDFs TO IPHONE OR IPAD
Once they are in your iTunes library on your computer, you'll then need to use iTunes to sync them to any of your iPhones, iPads, or iPods. Just select your device in iTunes, click on the Books tab, check the box to "Sync Books", and choose Apply to start a sync (when ready). This will add them to your iBooks application.
It's not possible to use iExplorer to transfer books or PDFs directly to the iBooks app. Even though iExplorer lets you add those EPUB folders or PDFs to the Media/Books directory where the iBooks files are stored in iOS, it won't update the database necessary for them to show up in the iBooks app.
For PDF files only, if you'd rather not sync them to your iPhone or iPad via iTunes, you could transfer them to our free iExplorer Mobile app (in the iOS App Store) which will let you move them to your iBooks app from there. Here is more information about our free companion app iExplorer Mobile:
Once iExplorer Mobile is installed on your device, you can add any files to it using iExplorer. To do this, just click on the iExplorer Mobile button on the Device Overview (Home) screen in iExplorer or go to the Apps section and open the iExplorer Mobile app folder from the alphabetical list. Then, open the Documents subfolder where you can add PDF files or entire folders via drag/drop or right-click and choose Add Files. Any files you add to the Documents folder will appear in the iExplorer Mobile app on your device.
Once the PDFs are in iExplorer Mobile, to then move them to the iBooks app, just open iExplorer Mobile on your device and tap on a PDF file to open it. Then, tap on Open In... (in the upper right corner) Another App Open in iBooks. However, you can only move them one at a time using this method.