The authors measured IR transmission spectra of two different concentrations of bacillus subtilis spores by using Fourier transform infrared spectroscopy (FTIR) technology. The mass extinction cross section k of bacillus subtilis spores was calculated according to Lambert-Beer law and the imaginary part ni of the complex refractive index was also calculated through k. The real part nr of the complex refractive index was derived from the KK (Kramers-Kronig) relationship and the experimental results were also analyzed and discussed with the study of measurement and analysis method of the complex refractive index on bacillus subtilis spores, it is of great significance to further research the absorption and scattering characteristics, and to broaden the measurement and remote sensing technology method of the biological aerosols.