The contents and distributions of metal elements in the brain are closely related to neurodegenerative diseases.In this study, we examined Fe, Cu and Zn contents in the brain section associated with Parkinson‘s disease(PD)using synchrotron radiation X-ray fluorescence(SRXRF). PD mouse model induced by 1-methyl-4-phenyl-1,2,3,6-terahydropyridine(MPTP) was used for the elemental analysis(e.g., Fe, Cu and Zn) in the substantia nigra pars compacta(SNpc) region of mice brain tissue samples. We found that mice in the MPTP group had higher contents of Fe, Cu and Zn in the SNpc than the control group. After treating the PD mice with rapamycin, the contents of Fe, Cu and Zn were reduced, the dopamine neurons and motor function were rescued correspondingly. The results prompted that the SRXRF provided an ideal method for tracing and analyzing the metal elements in the brain section to assess the pathological changes of PD model and the therapeutic effect of drugs.