Can I apply for EMRS PGT exam? I have special B.Ed and M.Com.

To qualify for PGT commerce, you need to hold a post-graduate degree in commerce along with a B.Ed. Having a B.Ed in Special Education does not pose an obstacle, so you are certainly eligible.

For PGT commerce one should be post graduate in commerce + B.Ed. So you are definitely eligible as B.Ed Special Education is not a hindrance.