The aim of this study was to explore the possible effects of iron deposition on the measurement of diffusion tensor imaging (DTI) metrics in deep gray matter nuclei in the normal human brain. Susceptibility-weighted imaging (SWI) and DTI were performed on nine MnCl2 phantoms and 85 healthy adults. The SWI phase value (PV) and DTI metrics including fractional anisotropy (FA), mean diffusivity (MD), radial diffusivity (RD), and axial diffusivity (AD) were measured in phantoms and the frontal white matter (FWM), caudate (CA), putamen (PU), and globus pallidus (GP) of both hemispheres in healthy adults. The FA correlated linearly with PV and MnCl2 concentrations in phantoms. The PV in the PU was positively correlated with age. The FA was negatively correlated with age in the FWM and positively correlated with age in the PU. AD positively correlated with PV in CA, PU, and GP. FA increased with elevated PV in the PU when controlling for the impact of age. The age-related increasing of PV, which predominantly caused by iron deposition, probably influences the measurement of DTI metrics in the PU in the normal human brain and should be considered when diagnosing various neurodegenerative diseases using DTI metrics.