The inter-tract/region dependencies of white-matter in Parkinson’s disease are usually ignored by standard statistical tests. Moreover, it remains unclear whether the disruption of white-matter tracts/regions suffices to identify Parkinson’s disease patients from healthy controls. A machine learning approach was applied to capture the interdependencies between white-matter tracts/regions and to differentiate PD patients from healthy controls. First, the mean regional white-matter profiles, including white-matter volume, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity, were extracted as features in Parkinson’s disease patients (N = 78) and in healthy controls (N = 91). Then, the feature selection and classification were performed using t-test and linear support vector machine, respectively. Last, the relationships between clinical variables and regional magnetic resonance indices were estimated. Our results showed the combined features (white-matter volume, fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity) had the best performance with an accuracy of 75.15% and area under curve of 0.8171, respectively. The most discriminative white-matter features were centered on the association fibers, commissural fibers, projection fibers, and striatal fibers. The discriminative regions of right anterior limb of internal capsule had positive association trends with the Unified Parkinson Disease Rating Scale III score; while the genu of corpus callosum and right retrolenticular part of internal capsule had positively association trends with the Hamilton Depression Rating Scale score. Our finding showed the multivariate machine learning approach is a promising tool to detect abnormal white-matter tracts/regions in Parkinson’s disease, and provides us a multidimensional means for neuroimaging classification.