This paper proposes the method of nanoscale microdisplacement modeling and control of the piezoelectric ceramic actuator (PCA) mounted on the end of a micro-nano robot. The robot works in the vacuum chamber of a Scanning Electron Microscope (SEM). We use the time-to-digital conversion (TDC) method to measure the displacement of the PCA. For the purpose of establishing the relationship of the applied voltage and the displacement of the PCA, we designed an online modeling and control system based on PC/104. Models with different order combinations are applied to fit the transfer function of the system and the least squares method is applied to identify the parameters of each model. In addition, the second-order transfer function model is used to approximate the open-loop transfer function model of piezoelectric ceramic by comparing the model fitting rate. Specially, some open-loop control experiments are performed to verify the accuracy of the model. Furthermore, a PID controller is proposed to achieve accurate position control for the PCA. In the end, simulation results demonstrate the feasibility and effectiveness of the closed-loop control system.