This study aims to explore whether the differences in static and dynamic functional connectivity (s-FC and d-FC) can serve as potential biomarkers of multiple system atrophy (MSA). 24 MSA patients and 20 normal controls (NCs) were enrolled. We applied both s-FC and d-FC to evaluate functional changes in MSA patients and calculated the graph theory attributes based on s-FC and d-FC. We found that there were significant correlations between indicators of s-FC and d-FC and clinical performance. Furthermore, the receiver operating characteristic (ROC) analysis revealed that the substantially different FC features can serve as predictors to distinguish MSA from NC.