Incorporating linear-scanning MEMS micromirrors into Fourier transform spectral acquisition systems can greatly reduce the size of the spectrometer equipment, making portable Fourier transform spectrometers (FTS) possible. How to minimize the tilting of the MEMS mirror plate during its large linear scan is a major problem in this application. In this work, an FTS system has been constructed based on a biaxial MEMS micromirror with a large piston displacement of 180 μm, and a biaxial H∞ robust controller is designed. Compared with open-loop control and PID closed-loop control, H∞ robust control has good stability and robustness. The experimental results show that the stable scanning displacement reaches 110.9 μm under the H∞ robust control, and the tilting angle of the MEMS mirror plate in that full scanning range falls within ±0.0014°. Without control, the FTS system cannot generate meaningful spectra. In contrast, the FTS yields a clean spectrum with an FWHM spectral linewidth of 96 cm-1 under the H∞ robust control. Moreover, the FTS system can maintain good stability and robustness under various driving conditions.