Parkinson’s disease (PD) is a neurodegenerative disorder characterized by cardinal motor symptoms and other non-motor symptoms. Studies have investigated various brain areas in PD by detecting white matter alterations using diffusion magnetic resonance imaging processing techniques, which can produce diffusion metrics such as fractional anisotropy and quantitative anisotropy. In this study, we compared the quantitative anisotropy of whole brain regions throughout the subcortical and cortical areas between newly diagnosed PD patients and healthy controls. Additionally, we evaluated the correlations between the quantitative anisotropy of each region and respective neuropsychological test scores to identify the areas most affected by each neuropsychological dysfunction in PD. We found significant quantitative anisotropy differences in several subcortical structures such as the basal ganglia, limbic system, and brain stem as well as in cortical structures such as the temporal lobe, occipital lobe, and insular lobe. Additionally, we found that quantitative anisotropy of some subcortical structures such as the basal ganglia, cerebellum, and brain stem showed the highest correlations with motor dysfunction, whereas cortical structures such as the temporal lobe and occipital lobe showed the highest correlations with olfactory dysfunction in PD. Our study also showed evidence regarding potential neural compensation by revealing higher diffusion metric values in early-stage PD than in healthy controls. We anticipate that our results will improve our understanding of PD’s pathophysiology.