White matter degeneration have been attributed to the motor and non-motor symptoms of Parkinson’s disease and atypical parkinsonism. Our study shows different pattern of white matter changes in multiple system atrophy and progressive supranuclear palsy compared to Parkinson’s disease. Furthermore, different affected areas of white matter changes were found among atypical parkinsonism. The involved regions are consistent with the understanding of the pathogenesis of the diseases. Our result proves that fixel based analysis is a robust technique to study white matter degeneration in PD and atypical parkinsonism.