The reflection of the optic system surface and the absorption of the infrared material could reduce the transmission of the incident light in spatially modulated Fourier transform infrared spectrometer. Through the calculation of the transmission function of the interference system and the simulation of the interferogram image and recovered spectrum affected by transmission function, it was indicated that the contrast of the interferogram image declined and the spectral line intensity weakened. The theoretical analysis shows that the contrast of the interferogram image was related to the intensity reflectance of the anti-reflection film, and the attenuation of the spectrum was determined by transmission efficiency concerned with intensity reflectance R1 of the anti-reflection film, intensity reflectance R2 of the beam splitter film, and the absorption coefficient. By means of the analysis and argumentation, the absorption of the material could be ignored in our investigative wave band. So the transmission efficiency was determined only by R1 and R2. Then taking the transmission efficiency as the design target, according to the transmission required by system, the tolerance of the R1 and R2 could be gained.