In charging control system of trolley bus, the output performance of the control system would be unstable caused by external turbulent, which results in the noise amplified. To enhance the robust and adaptive of control system, a new no-linear control method was proposed based on tracking differentiator to improve the charging control performance of ultra-capacitor trolley bus and optimize the curve of the output current and voltage of the system. Aiming at the problem of control parameter variety, a Ziegler-Nichols method was used to adjust the parameter. Simulation and test results completely proved that the proposed method was effective, which improved performance of the control system apparently, solved the contradiction between rapidity and overshoot, and realized quick and smooth charging for the super-capacitor energy storage trolley bus.