To link to an EPUB (.epub) in Apple Books, first you need to know the book’s asset ID. Control-click (or right-click on Windows) the book on Apple Books and copy the link. In the example below, the asset ID is 335522876:
https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewMetaBook?cc=us&id=335522876&mt=13
An Apple Books link to this book would be:
ibooks://assetid/335522876
Note that linking to a specific part of a different book is only supported for books created with iBooks Author. If you use the asset ID of an EPUB and specify a page number, the EPUB will open, but not to the correct page. Links that include the asset ID can be used on other apps such as Mail and iTunes U. The links will open in Apple Books.