Micro-electro-mechanical system (MEMS) has great potential application in biomedical field. The piezoelectric drive system based on piezoelectric ceramics plays an important role in the field of high-precision control of micro-nano operation. In the practical application of various fields, the interaction between micro system and environment is always a hot research direction. Since the tracking force error at the micro scale is more non-negligible than that at the macro scale, the precise control of the contact force between the micromanipulator and the environment is the key to improve the accuracy of the micro operation. Therefore, a force tracking impedance control strategy is proposed in this article, which can accurately track the contact force during operation. Because the impedance model requires high environmental parameters, an extended Kalman filter is proposed to estimate the external environmental parameters online. Experimental results show that the proposed control method can successfully realize the force tracking control of the micro-manipulator environment interaction model and has good tracking accuracy. The average absolute error of force tracking is 7. 82 mN, and the root mean square error is 10. 16 mN. Therefore, the method is feasible to accurately track the contact force in uncertain environment.