A system and method for motion control of a humanoid robot are provided. The system includes a remote controller for recognizing three-dimensional image information including two-dimensional information and distance information of a user, determining first and second reference points on the basis of the three-dimensional image information, calculating variation in angle of a joint on the basis of three-dimensional coordinates of the first and second reference points, and transmitting a joint control signal through a wired/wireless network. The system also includes a robot for checking joint control data from the joint control signal received from the remote controller and varying an angle of the joint to move according to the user's motion.