The collimation error in Fourier transform spectrometer has many effects on the interferogram and the spectrogram. By means of modulation, the authors found the reverse of contrast in the interferogram and the side slope noise in the spectrogram due to the collimation error. The authors analyzed the signal-to-noise ratio and resolution at different factor of beam divergence. When the factor of the beam divergence is 0.15°·mm-1, the signal-to-noise ratio can reduce to 6 dB and the resolution can go bad to 13.4 cm-1.