An automatic door operator and a drive mechanism thereof are disclosed. The drive mechanism of the automatic door includes a planetary reducer driven by an electric motor, and a drive shaft driven by a planetary reducer. The planetary reducer includes a housing and a planetary gear train mounted in the housing. The planetary gear train includes a final-stage planet carrier configured to output torque, and a center of the final-stage planet carrier is provided with a torque output hole. A first end of the drive shaft is detachably inserted in the torque output hole and is non-rotatably connected to the torque output hole, and a second end of the drive shaft extends out of the housing. The drive mechanism of the automatic door operator is advantageous to the miniaturization design of the automatic door operator.