Can The President pardon a military sentence?

Military Law is different than Civilian law, but the president being Comander-in-chief of the US Armed forces and having the power to pardon can he can do it for a military sentence? Say Bush doing it for the Soliders that mistreated the guantanamo bay POWs

Yes.

I believe that the President’s pardon authority extends to any criminal matter arising under federal law.

According to the Justic Departmentthe POTUS can pardon military convictions.

Not only can he, he does so fairly routinely. See here and here.