LEGO Marvel Super Heroes includes some new powers and abilities as well, however. For example, heat-related characters can destroy gold bricks, rocket-using characters can destroy silver bricks, superheroes that have the power of flight in the comic books can fly in the game, and characters with super strength can destroy or manipulate LEGO objects that normal characters cannot. LEGO Marvel Superheroes also carries over a large number of features that were included in LEGO Batman 2: DC Superheroes.

In addition, there are a variety of side-levels to embark on. The player progresses through a number of levels following a linear plot(in total 20), but can return to the levels later on in free play mode, using any of the characters they unlocked up until that point. Like a majority of the LEGO games created by TT Games, players take control of characters that are modeled like actual LEGO parts (but with far more mobility) and are divided into groups according to certain skills.