I am into 2nd month after hair transplantation. Is it safe to apply lemon juice to get rid of the dandruff?

It is not clear why you would want to put lemon juice on your head or why you believe it may help with dandruff.  You can consider using anti-dandruff shampoo.

I am not familiar with using lemon juice for dandruff. While it probably won't hurt your follicles anything like this are things you should run by your treating physician since they have their own list of things to do and to avoid.

At this time you can do whatever you want as everything is healed by this time. Lemon juice will not harm the area.