To decrease the distortion of the recovered spectrum, improve the quantity of the recovered spectrum and decrease the influence of the phase error of the new spectrum detection system based on MEMS (micro-electro-mechanical systems) micro-mirrors, a new phase error correction method for this system is proposed in the present paper. The source of phase error of the spectrum detection system based on MEMS micro-mirrors is analyzed firstly. The analyzed result indicated that the phase error of the new spectral Fourier transform detection system is the zero drift of the optical path difference, and the phase error can be corrected by Zero-crossing sampling which is realized by improving the structure of the interferometer system and Mertz product. The spectrum detection system is set up and the phase error correction method is verified by this system. The experiment result is show that the quantity of the recovered spectrum of the spectrum detection is improved obviously by using the improved interferometer system and Mertz product, and the recovered spectrum has no negative peaks and the side lobes is suppressed markedly. This correction method can reduce the influence caused by phase error to the system performance well and improve the spectral detection performance effectively. In this paper, the origin of the system phase error based on the new MEMS micromirror Fourier transform spectroscopy detection system is analyzed, and the phase error correction method is proposed. This method can improve the performance of the spectrum detection system.