Background Patients with Parkinson’s disease (PD) have elevated levels of brain iron, especially in the nigrostriatal dopaminergic system. The purpose of this study was to evaluate the iron deposition in the substantia nigra (SN) and other deep gray matter nuclei of PD patients using quantitative susceptibility mapping (QSM) and its clinical relationship, and to explore whether there is a gradient of iron deposition pattern in globus pallidus (GP)–fascicula nigrale (FN)–SN pathway. Methods Thirty-three PD patients and 26 age- and sex-matched healthy volunteers (HVs) were included in this study. Subjects underwent brain MRI and constructed QSM data. The differences in iron accumulation in the deep gray matter nuclei of the subjects were compared, including the PD group and the control group, the early-stage PD (EPD) group and the late-stage PD (LPD) group. The iron deposition pattern of the GP–FN–SN pathway was analyzed. Results The PD group showed increased susceptibility values in the FN, substantia nigra pars compacta (SNc), internal globus pallidus (GPi), red nucleus (RN), putamen and caudate nucleus compared with the HV group (P < 0.05). In both PD and HV group, iron deposition along the GP–FN–SN pathway did not show an increasing gradient pattern. The SNc, substantia nigra pars reticulata (SNr) and RN showed significantly increased susceptibility values in the LPD patients compared with the EPD patients. Conclusion PD is closely related to iron deposition in the SNc. The condition of PD patients is related to the SNc and the SNr. There is not an increasing iron deposition gradient along the GP–FN–SN pathway. The source and mechanism of iron deposition in the SN need to be further explored, as does the relationship between the iron deposition in the RN and PD.