The Super-Twisting control algorithm is adopted to analyze the U model based nonlinear control system in order to solve the controller design problems of non-affine nonlinear systems. The non-affine nonlinear systems are studied, the neural network approximation of the nonlinear function is performed, and the Super-Twisting control algorithm is used to control. The convergence of the Super-Twisting algorithm is proved by selecting an appropriate Lyapunov function. The Matlab simulation is carried out to verify the feasibility and effectiveness of the described method. The result shows that the output of the controlled system can be tracked in a very short time by using the designed Super-Twisting controller, and the robustness of the controlled system is significantly improved as well.