This paper presents a compound control system for precise control of the flame-retardant 4 (FR4)-based electromagnetic scanning micrograting. It mainly consists of a frequency controller and an angle controller. A dual closed-loop structure consisting of a current loop and an angle loop was designed in the angle controller. In addition, the incremental proportional–integral–derivative (PID) control algorithm was designed in the current loop, and the fuzzy-PID control algorithm was employed in the angle loop. From the experimental results, the frequency controller can effectively track the real-time resonant frequency of the scanning micrograting with a tracking accuracy of 0.1 Hz. The overshoot of the scanning micrograting is eliminated. Compared to an open-loop control system, the control system presented in this work reduces the steady-state error of the scanning micrograting from 1.122% to 0.243%. The control accuracy of the compound control system is 0.02°. The anti-interference recovery time of the scanning micrograting was reduced from 550 ms to 181 ms, and the long-term stability was increased from 2.94% to 0.12%. In the compound control system presented in this paper, the crucial parameters of the FR4-based electromagnetic scanning micrograting, including motion accuracy, anti-interference ability, and long-term stability, were effectively improved.