To realize the non-contact inspection and treatment of human gastro-intestines, a control system with bi-directional Radio Frequency(RF) was designed for a micro robot to heat the cancer of colon. First, the modules of control system and its hardware configuration were established.Then, the software program was completed and the movement control was efficiently implemented according to the timing sequence presented in this paper. Moreover,a driving mechanism was used to simulate the inchworm movement and the generalized predictive control algorithm of PID was introduced into the heat therapy. The control of a micro turning table could provide 0~360° positioning of cameras to show the video of colon tube in rotation. Finally, the system performance was tested as well. Experimental results indicate that the average RF communication time is 0.6 s and the step of the robot movement is continuum and stable. The angle of camera view can be changed from 0° to 360°, and the heat treatment can be stabled in 70 s. The experimental results demonstrate the effectiveness and reasonability of this control system and it satisfies the system requirements of real time inspection and thermal therapy for colons.