The problem of detecting the biological aerosol at low elevation angle is analyzed and discussed by using MODTRAN model. First of all, the atmospheric model and profile of MODTRAN model are introduced for the biological aerosol detection by Fourier transform infrared (FTIR) spectroscopy. According to the passive detection of biological aerosol by FTIR spectroscopy, the radiation brightness difference L between the background and the target biological aerosol is calculated by using the radiative transfer theory and the simplest three-layer model. The signal value 2Lt under the actual circumstance is derived from the derivative of L combined with the noise equivalent spectral radiance value of the spectrometer. Finally, the detection limit of biological aerosol for each atmospheric mode is predicted with the passive remote sensing method. The limit concentration of detection for each atmospheric mode is different due to the differences in boundary layer temperature, transmittance, and background radiation brightness of atmospheric model, and it is also related to the absorption coefficient of biological aerosol. It is shown that the passive remote sensing of FTIR technology can detect the presence of the biological aerosol. Therefore, the detection of the biological aerosol is feasible. It presents a method of detecting the biological aerosol cloud under the actual circumstance.