Structure of biological molecules may change when exposure to electromagnetic field, the change can be recognized from the change of the infrared spectrum. The present paper studied microstructure of rat blood, testis and brain after its exposure to infrared light for 30 days via their FTIR characteristics within the 1 700～1 000 cm-1 range, and the authors also analysed biological characteristics of tissue microstructure with infrared light exposure on rat by their second derivative spectra. Mechanisms of biological effects induced by infrared light were further explored through the findings. All the results indicate that the Fourier transform infrared spectroscopy can be used to analyze infrared light exposure for biological tissue microstructure.