This paper presents an autonomous navigation system for cost-effective magnetic-assisted colonoscopy, employing force-based sensors, an actuator, a proportional–integrator controller and a real-time heuristic searching method. The force sensing system uses load cells installed between the robotic arm and external permanent magnets to derive attractive force data as the basis for real-time surgical safety monitoring and tracking information to navigate the disposable magnetic colonoscope. The average tracking accuracy on magnetic field navigator (MFN) platform in x-axis and y-axis are 1.14 ± 0.59 mm and 1.61 ± 0.45 mm, respectively, presented in mean error ± standard deviation. The average detectable radius of the tracking system is 15 cm. Three simulations of path planning algorithms are presented and the learning real-time A* (LRTA*) algorithm with our proposed directional heuristic evaluation design has the best performance. It takes 75 steps to complete the traveling in unknown synthetic colon map. By integrating the force-based sensing technology and LRTA* path planning algorithm, the average time required to complete autonomous navigation of a highly realistic colonoscopy training model on the MFN platform is 15 min 38 s and the intubation rate is 83.33%. All autonomous navigation experiments are completed without intervention by the operator.