BACKGROUND: Parkinson's disease (PD) and Multiple system atrophy-parkinsonian type (MSA-P) both belong to α-synucleinopathies. Their overlapping clinical manifestations often lead to misdiagnosis. This study aimed to identify objective neuroimaging biomarkers for differentiating PD from MSA-P. METHODS: 25 PD patients, 20 MSA-P patients, and 20 healthy controls (HC) were enrolled. All participants underwent resting-state functional magnetic resonance imaging (rs-fMRI). Differences in the amplitude of low-frequency fluctuation (ALFF) across brain regions between the PD and MSA-P groups were analyzed, and the discriminative ability of ALFF alterations was evaluated. RESULTS: Compared to MSA-P patients, PD patients exhibited significantly reduced ALFF in the bilateral cerebellum, left occipital lobe, bilateral cingulate cortex, and right hippocampus (all P < 0.05). Receiver operating characteristic (ROC) curve analysis demonstrated that the ALFF alterations in the right cerebellar subregions (Cerebellum_3_4_5_R/Cerebellum_10_R) achieved an area under the curve (AUC) of 0.900 for distinguishing PD from MSA-P. CONCLUSIONS: Our study provides new insights into ALFF alterations in specific brain regions of PD and MSA-P patients using rs-fMRI, offering a theoretical basis for exploring their distinct neural mechanisms. Furthermore, we identified that ALFF changes in the right cerebellar subregions serve as a potential imaging biomarker for differentiating PD from MSA-P.