Multiple system atrophy (MSA) is regarded as a progressive neurodegenerative disease mainly divided into MSA-p type with Parkinsonism and MSA-c type with cerebellar ataxia as the main symptom. However, its neural mechanism is still unclear. In this study, we only focus on the MSA-c type. The purpose of this study is to explore the functional connectivity changes of the cerebello-cortical circuit in MSA-c type by using resting state functional magnetic resonance imaging (rs-fMRI). Thirty-six subjects (18 MSA and 18 normal controls) participated in this study and the rs-fMRI data were collected by applying resting state amplitude of low-frequency fluctuations (ALFF), we found the significant decreased ALFF in the MSA patients relative to controls, which included left cerebellum 8 area, 9 area, 7b area and Cru1 as well as vermis 7. Then we select the brain region of cerebellum 8 area as seed to investigate whole brain functional connectivity alteration in the MSA patients. When comparing to controls, several regions showed decreased connectivity in the MSA patients including bilateral cerebellum anterior lobe, left cerebellum posterior lobe, left dentate, bilateral pons, inferior parietal lobule (IPL), lingual gyrus (LG), parahippocampus (PHG), and middle temporal gyrus (MTG). In addition, there were closely correlation between functional connectivities and clinical performances in the MSA patients. The current study confirmed that the disrupted functional connectivity of specific cerebello-cortical circuit in the MSA patients, which is responsible for the clinical performances.