Due to the precision restriction of the system assembling and device location, the relative position of the two stepped micro-mirrors in spatial modulation Fourier transform spectrometer can appear the shift and rotation in the alignment process. Using the linear system theory and scalar diffraction theory, the model of the interferogram image and recovered spectrum corresponding to shift error and rotation error are established respectively. By means of the analysis to the calculation result, the marginal interferogram units are clipped by the shift error and rotation error, and the concomitant spectrum lines is appeared in recovered spectrum, bringing the spectrum noise badly. Finally, according to the action characteristics of the shift error and rotation error to interferogram image, a method of regional compensation to interferogram image is put forward, by extending the step number of two stepped micromirrors to expand the interference area, then using the internal effective interferogram units to recover the signal spectrum. Calculation shows that this method can restrain the influence of the alignment error effectively, and so as to decrease the location precision of the stepped micro-mirror consumedly.