While the gameplay was typical of the Marvel vs. Capcom series, Marvel vs. Capcom was distinguishable by two features: the ability to summon assist characters, and the Duo Team Attack.

Unlike the previous game in the series, the point character of a Marvel vs. Capcom team could not summon the offscreen partner for an assist attack; instead, an assist character was randomly selected before the match began. This character could be summoned a limited number of times in battle to attack the opponent in parallel. Codes could be used to force the system to select a certain assist character.

The Duo Team Attack allowed a player to control both characters on his or her team simultaneously for a brief period of time; the characters had unlimited use of their super moves during this time. Since some characters had hard-to-avoid super moves that did substantial damage if blocked, the Duo Team Attack led to tactics that were oriented around activating it before your opponent could. Since the PlayStation port only allowed one character to play a point, a Duo Team Attack would call the assist character repeatedly without cost during its duration.