This study evaluated the impact of radiofrequency coil selection and spatial inhomogeneity correction on susceptibility source separation imaging in the brain. Ten healthy participants were scanned on a 3 T magnetic resonance imaging system using both 20-channel and 64-channel coils. Susceptibility measurements of deep gray matter nuclei were compared before and after spatial inhomogeneity correction. Prior to correction, significant differences were observed across multiple deep gray matter nuclei between the two coils (P < 0.05). After correction, these differences were no longer significant (P > 0.05), and the correlation coefficient for diamagnetic susceptibility increased to 0.87. These findings demonstrate that spatial inhomogeneity associated with high-channel-count phased-array coils can introduce substantial bias in susceptibility source separation, whereas inhomogeneity correction effectively mitigates such hardware-related bias.