This paper focuses on improving tracking performance of totally uncoupled compliant micromanipulator based on robust control method of elliptical hysteresis model. The hysteresis model and hysteresis compensation model for proposed mechanism based on Piezoelectric transducer (PZT) are established by using elliptical model method. The values of elliptical hysteresis model parameters are identified by simulating method with different frequencies of control input. The uncertainty model is also established, the values of corresponding estimated parameters are conformed by experiment method. Based on the uncertainty model and elliptical hysteresis model, the robust tracking control method is presented and utilized to evaluate the tracking performance of proposed mechanism under inputting different tracking curves. The proposed method can accurately control the output displacement and improve tracking performance of this mechanism, which are validated and carried out by using experimental studies. Additionally, the coupling errors between two directions are kept within 0.14% and the tracking errors for different curves are within 2.5%.