The performance of the uniform motion of the moving mirror, which is the only constant motion part in FTIR spectrometer, and the performance of the alignment of the fixed mirror play a key role in FTIR spectrometer, and affect the interference effect and the quality of the spectrogram and may restrict the precision and resolution of the instrument directly. The present article focuses on the research on the uniform motion of the moving mirror and the alignment of the fixed mirror. In order to improve the FTIR spectrometer, the maglev support system was designed for the moving mirror and the phase detection technology was adopted to adjust the tilt angle between the moving mirror and the fixed mirror. This paper also introduces an improved fuzzy PID control algorithm to get the accurate speed of the moving mirror and realize the control strategy from both hardware design and algorithm. The results show that the development of the moving mirror motion control system gets sufficient accuracy and real-time, which can ensure the uniform motion of the moving mirror and the alignment of the fixed mirror.