For the multiple imaging by the microlens array and the distributed phase modulation by the micromirror array, the snapshot Fourier transform imaging spectrometer can acquire image and spectrum information in real time. Limited by the fabrication accuracy of array devices, the structural parameters of the units in the microlens array and the micromirror array display different degrees of deviations, which affects the system performance. The structural parameter deviations of the lens units in the microlens array can be equated with the non-uniformity of the focal length, and the differences among the step units in the micromirror array are mainly reflected in the non-uniformity of the step length. A model of optical field propagation with non-uniform errors was built according to the phase modulation characteristics of the microlens array and the micromirror array on the optical field. The Monte Carlo method was used to synthesize the non-uniform errors of the focal length of the microlens array and the step length of the micromirror array. Statistical analysis showed that the relative spectrum error increased monotonously with the increase in the standard deviations of the focal length and the step length. Given the non-uniform error of the step length, a spectrum correction method of discrete spectrum phase compensation was proposed. The method effectively reduced the fabrication accuracy requirement on the micromirror array and improved the quality of the recovered spectrum.