In order to study the effect of radiation dose to rare traditional Chinese medicine composition, Fourier transform infrared spectra and their second derivative spectra of Hippocampus trimaculatus Leach powder irradiated by  0, 1.5, 3, 4.5, 6, 9,12，15, 18, 19.5 and 21 kGy were studied. Protein is the main component of Hippocampus trimaculatus Leach powder, and the content is more than 70%. It was shown that the infrared spectrum  of the protein and lipid absorption in sample band doesn〖KG-*4〗’t change when it was irradiated by 1.5, 3, 4.5 and 6 kGy. But the infrared spectrum of sample had obvious change when it was irradiated by higher than 9 kGy in intensity; Irradiation had little effect on the protein secondary structure of sample if irradiation is not more than 9 kGy; Irradiation had greater effects on the protein secondary structure if it is higher than 9 kGy. It is feasible if Hippocampus trimaculatus Leach powder was irradiated by no more than 9 kGy. Research results provides a reference on  irradiation dose setting of Hippocampus trimaculatus Leach powder for nuclear irradiation  companies.