In this paper, 10 resonant modes were divided based on the structure of a specific two-dimensional electromagnetic micromirror from Professor Shen’s team and Finite Element Method (FEM), and using as many as 10 resonant modes to do such analysis was the first time according to the best of our knowledge. The results showed that the slow axis can participate in several resonant motions under the signals of resonant frequencies. In particular, participating in Mode 1 for slow-scan axis was the key reason to the instability of Vertical Refreshing Scanning (VRS) in raster scanning. In addition, a piecewise PID control based on filters design for this electromagnetic micromirror was proposed to suppress the unexpected resonant oscillation and to improve the angular positioning accuracy in slow-scan axis control. Finally, the proposed method was applied to electromagnetic micromirror stages, and the experimental results showed that the proposed approach was reliable.