What is the best way to prepare for M.Sc after completing B.Sc in agriculture?

You should simply study your B.Sc syllabus thoroughly and also keep fair knowledge of general science. Pay special attention to the subject of interest in M.Sc. You can also prepare for JRF if you want a good college and scholarship. Just focus on your B.Sc syllabus.

Whichever field of agriculture you are interested in for your Master's degree, you have to score a higher CGPA/OGPA in your Bachelor's degree and then clear the entrance exam (if any in the admission procedure). Revise well all the coursework plus recent development in agriculture.