Objective To use resting?state functional magnetic resonance imaging （rs?fMRI） to study amplitude of low?frequency ?uctuation （ALFF） and regional homogeneity （ReHo） changes in brain function in patients with anti?N?methyl?D?aspartate receptor encephalitis with cognitive impairment （ANMDARE?CI）. Methods A total of 33 patients with anti?N?methyl?D?aspartate receptor encephalitis （ANMDARE） and 18 healthy volunteers （Controls） underwent rs?fMRI， the Beijing version of the Montreal Cognitive Assessment （MoCA?B） and neuropsychological scales. The cognitively impaired （ANMDARE?CI， n = 17） and the cognitively normal （ANMDARE?CN， n = 16） were divided according to the assessment of the MoCA?B scale. Differences in brain activity between the ANMDARE?CI， ANMDARE?CN and control were analysed using ReHo and ALFF. One?way ANOVA was performed using SPM12， ReHo and ALFF values for differential brain regions were extracted for independent samples t?tests for two?way comparisons and correlation analysis between clinical data and ANMDARE scales. Results Compared with ANMDARE?CN and Control， in ANMDARE?CI，ALFFs of bilateral cerebellar were reduced， and the right superior frontal gyrus and left central anterior gyrus ALFF were increased （P < 0.01）. Compared to Controls， in ANMDARE?CI and ANMDARE?CN， ALFFs of bilateral thalamus and ReHo of the right anterior cerebellar lobe were decreased （P < 0.01）. ReHo of Left Anterior Cingulate in ANMDARE?CN was significantly lower than ANMDARE?CI and Controls （P < 0.01）. Increased ALFF values on the right superior frontal gyrus were inversely correlated with MoCA?B performance scores （r = -0.586， P = 0.013）. Increased left central anterior gyrus ALFF was negatively correlated with the MoCA?B directional score （r = -0.668， P = 0.003） and positively correlated with HAMA （r = 0.665， P = 0.004）. No correlation between ReHo values and clinical data was found （P > 0.016）. Conclusions Abnormal brain function in ANMDARE_CI may be associated with altered spontaneous cerebellar activity.