Marvel Super Heroes is a 2D fighting game and the second Capcom title to feature characters from the Marvel comic universe. The gameplay is very similar to X-Men: Children of the Atom, but with a simplified Super Combo gauge and the addition of infinity gems. Each character starts with a set of gems. These can be activated during a fight to improve speed, power and defence, or provide special abilities to create crushing stone walls, open up a rift in space, or reverse the opponent's controls. The use of the gems is inspired by the The Infinity Gauntlet comic book series.

There are ten playable characters. The heroes are Captain America, The Incredible Hulk, Iron Man, Psylocke, Spider-Man and Wolverine. The villains are Blackheart, Juggernaut, Magneto and Shuma-Gorath. Anita from the Darkstalkers series is a hidden character in the Japanese version. The bosses are Doctor Doom and Thanos. During the boss fight Thanos steals all the player's gems (except for mind) and uses them with new effects.