Nonthermal effects of extremely low frequency electromagnetic fields (ELF-EMF) are related to changes in the microstructure of biological tissues after exposure to electromagnetic radiation. Fourier transform infrared spectroscopy (FTIR) analysis method can effectively study the mechanisms of biological effects of electromagnetic radiation. The present paper studies the characteristics of sensitive tissues of rat after ELF-EMF exposure. FTIR analysis of sensitive tissues of control group and experimental group showed that 50 Hz, 0.75 mT ELF-EMF exposure for 20 days can affect molecular level of the rat testis, blood and brain. Experimental results show that regular changes in absorption peak positions and intensity in the spectra of sensitive tissue may be caused by exposure to ELF-EMF, therefore, Fourier transform infrared spectroscopy is an effective means to study mechanism of biological effects of electromagnetic fields.