A cleaning mechanism of a 3D printer including a cleaning module, a first wiper, a second wiper, and a carrier is provided. The cleaning module has a top plane. The first wiper is arranged corresponding to the cleaning module and protruding beyond the top plane. The second wiper is arranged on the cleaning module and protruding beyond the top plane. The carrier is connected to a rail and suspended above the cleaning module. A modeling nozzle corresponding to the first wiper and a painting pen corresponding to the second wiper are arranged on the carrier and movable. The modeling nozzle and the painting pen are arranged respectively aligned to the first wiper and the second wiper. The modeling nozzle is allowed to move pass the first wiper and bypass the second wiper. The painting pen is allowed to move pass the second wiper and bypass the first wiper.