For further research on the microparticles trajectory in the process of micromanipulation, the paper modeled on the coupling dynamic of three-degree-of-freedom micromanipulator which is based on piezoelectric ceramic. In the micromanipulation, the transformation of certain movement direction can generate a corresponding change in the coupling in three-degree-of-freedom micromanipulator movement, the fuzzy PID method was adopted by the control system of this study, and the modeling analysis was performed on the control system. After completing the above modeling, the simulation model is built by the MATLAB Simulink software. The simulation output results are basically in accordance with the actual trajectory, which achieve the successful research purposes of coupling dynamics model for three-degree-of-freedom micromanipulator and application of fuzzy PID method.