Clinically differentiating multiple system atrophy cerebellar (MSA-C) phenotype and spinocerebellar ataxias (SCAs) is challenging especially in the early stage. We assessed diagnostic value of brain magnetic resonance imaging (MRI) in differentiating MSA-C and SCAs based at different disease stages (<3, 3-7, and >7 years of disease duration). Overall, 186 patients with probable MSA-C and 117 with genetically confirmed SCAs were included. Hot cross bun (HCB) signs and middle cerebellar peduncle (MCP) hyperintensities were exclusively prevalent in MSA-C compared to SCAs at <3 years (HCB, 44.6% versus 0.9%; MCP hyperintensities, 38.3% versus 0.9%, respectively). Sensitivity, specificity, and positive predictive value (PPV) for HCB signs to differentiate MSA-C from SCAs were 45%, 99%, and 99% and those for MCP hyperintensities were 68%, 99%, and 99%, respectively; considering both HCB signs and MCP hyperintensities, specificity and PPV were 100%. However, the differential value of MRI signs decreased over time. MCP widths were smaller and showed more significant decrease in MSA-C than in SCAs. In conclusion, pontine and MCP changes were exclusively prominent in early stage MSA-C rather than in SCAs. Therefore, we should consider disease duration when interpreting pontine and MCP changes in brain MRIs, which will help better differentiate MSA-C and SCAs.