The invention relates to an intelligent auxiliary positioning orthopedic surgery robot system and an operation method thereof. The system comprises a robot, a control module for controlling the robot to move, coarse positioning and fine positioning, and terminal service equipment, wherein the robot comprises a base, a lifting mechanism, a lifting rod, a four-section arm, a surgery bed, a camera, a touch screen, a torque sensor and a positioning marking assembly; the control module comprises a motion control module, a coarse positioning module and a fine positioning module; and the terminal service equipment comprises the touch screen, an operation console, a real-time monitoring module and a result storage and output module. The intelligent auxiliary positioning orthopedic surgery robot system is high in intelligent degree, a positioning navigation function can be achieved in an orthopedic surgery, the system precision is high, the positioning accuracy is guaranteed through a coarse positioning and fine positioning mode, the robot serves as an intelligent surgical tool to assist a doctor in completing the surgery, and the quality of the whole surgery is greatly improved.