Precise differentiation between MSA subtype is critical in medical intervention and prognosis. The results of previous studies using DTI to differentiate subtypes of MSA is controversial. We use fixel based analysis to examine the tract-specific differences in white matter between individuals with MSA and healthy controls. The results demonstrate the white matter degeneration in specific fibre bundle, including middle cerebellar peduncle, pontine crossing tract and cerebellar white matter tracts in the early MSA-C patients; in contrast, this pattern was not observed in MSA-P patients. This suggests that FBA may be a sensitive marker for early differential diagnosis of MSA subtype.