We separated this year my spouse is on SSI and Medicaid, will he be affected if we file jointly?

Are you still married and living separately, or are you divorced?

still married and living separately

You can file jointly without affecting his SSI or medicaid.  If you file jointly, you will need to enter his SSA-1099 (if he receives one) on your return.

what is an ssa 1099

It's the form sent to the recipients of Social Security benefits.  It's a long paper with pink (or red) boxes on it that comes from the SSA.

He did not receives it are you sure he will not loose his SSI and Medicaid if we fille jointly. ( big difference for me )

If he is receiving SSI for a disability, he will not lose it by filing a joint return.  It is not based on income, but on his disability.  However, if you remain uncertain, you can contact the SSA and ask them.