From the Super Mario Wiki
Mask Koopas are Koopa Troopas that wear bizarre masks that resemble Mario. They appear only after the player beats the Special World in Super Mario World. Their masks function identically to Shells, they come off when pounded, can be thrown at enemies, and can provide Yoshi with special powers.
As seen in a cut scene in Super Mario World: Super Mario Advance 2, Mask Koopas apparently got their masks when Luigi was throwing them down from a balloon. The Koopa Troopas were missing their shells, so they decided to take these masks to replace the shells.
Some Mask Koopas have wings sprouting from their masks, making them the equivalent of Koopa Paratroopas after losing their shells. Like Paratroopas, one stomp removes their wings, turning the creatures into normal Mask Koopas. Also affected are Kamikaze Koopas who now resemble flashing and spinning Mario heads.
Mask Koopas act no differently from the basic Koopa Troopas - however, where the Red and Green Koopa Troopas were, Blue and Yellow Mask Koopas will be in their place. Red and Green Shells are also replaced by Blue and Yellow Shells. Red and Green Koopa Paratroopas are unchanged, keeping their color. They have yet to appear in any other game besides Super Mario World, excluding remakes.