Unlike past Sonic the Hedgehog games, Sonic Heroes is the first Sonic game that allows the player to control three characters at once (although the player controls the selected character, while the computer takes control of the remaining two characters). A player will choose one of four teams to use. The four teams all have their own strengths and weaknesses as do each of the individual characters. Sonic Heroes was the first Sonic game to introduce the "Speed, Flight, and Power" concept into the series.

A team is made up of three characters, each suited for a specific task. The three types of characters are "flight," "speed," and "power." The flight type is able to ascend short distances with other party members. The speed character has the ability to move at a faster rate than the other two members of the team. Lastly, the power character is the strongest physically of the three.