I am currently in TPS and my employer said he will apply for my EB2 ASAP. So I only have 12 months left. Do you think it is wise to apply for EB2 now. I have bachelors and masters degree. My concern is that I might not get EAD in this 12 moth and the application is a waste. Resulting in visa denial from immigration officer in Nepal saying I had intent to stay, if I ever wanted to do come back in US for phd after my TPS expires.

You have about 13 months. If you start ASAP, labor certification takes about 8 months (on average, and assuming it doesn't get audited). Once labor certification is approved, you can file I-140 and pay for expedited processing which takes about 15 days to get approval. Then you may file for I-485 (along with the application for EAD and travel document which should normally be approved within three months). With that being said, consult the lawyer for your employer to see what they suggest.