BackgroundNeuropsychiatric manifestations, such as cognitive impairment, are relatively prevalent in systemic sclerosis (SSc) patients. This study aimed to investigate the resting state (RS) functional alternations of SSc patients and the potential influenced factors.MethodsForty-four SSc patients (mean age, 46.3 ± 11.4 years; 40 females) and 19 age and sex comparable healthy volunteers (mean age, 42.6 ± 11.3 years; 16 females) were recruited and underwent RS functional MR imaging (fMRI) and neuropsychological assessments. Functional segregation analysis was performed to calculate the amplitude of low frequency fluctuation (ALFF) and regional homogeneity (ReHo). Functional integration analysis was conducted using group independent component analysis to calculate intra-network and inter-network functional connectivity (FC). The fMRI measurements were compared between SSc patients and healthy volunteers using voxel-based pairwise two-sample t-tests. The correlations between clinical characteristics and fMRI measurements were also analyzed.ResultsCompared to healthy volunteers, SSc patients exhibited significantly decreased ALFF and increased ReHo (all P < 0.01, FWE corrected). SSc patients predominantly showed decreased intra-network and inter-network FC in the auditory network, visual network, default mode network, frontoparietal network and attention network (intra-network FC: P < 0.01, uncorrected, cluster size > 30; inter-network FC: P < 0.05, FDR correction). Furthermore, clinical characteristics including disease duration (r value ranged from − 0.31 to 0.36), elevated erythrocyte sedimentation rate (r = 0.35), Montreal Cognitive Assessment score (r = 0.43), and Hamilton Depression Scale score (r = -0.40) were significantly associated with fMRI measurements (all P < 0.05).ConclusionsSpontaneous activity and functional connectivity alternations can be seen in SSc patients, which are partially associated with neuropsychiatric manifestations and tend to aggravate with disease duration.