Background The aim of the current study was to explore the characteristics of cerebrospinal fluid (CSF) cytology in anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis.Methods CSF was collected from patients with anti-NMDAR encephalitis at Peking Union Medical College Hospital and Henan Provincial People’s Hospital from 01 January 2015 to 31 December 2018, and cytological characteristics and other parameters of the CSF were analyzed.Results CSF cytological data were obtained from 164 patients with anti-NMDAR encephalitis. Visible signs of inflammation were identified in cytological analyses of 112 patients’ CSF, including 46 cases of mild inflammation, 58 of moderate inflammation, and 8 of severe inflammation. With regard to inflammation type, 89 cases were classified as lymphocytic inflammation, 22 as mixed inflammation with both lymphocytes and neutrophils, and 1 case was classified as mixed inflammation with lymphocytes, neutrophils, and eosinophils. Activated lymphocytes were detected in 51 patients, and plasma cells were detected in 16. Oligoclonal bands were detected in 111/164 patients, and 51 patients were positive for specific oligoclonal bands in CSF. The positivity rate was 45.9%. In comparison with routine CSF examination with an inflammation positivity threshold of > 5 × 10 6 cells/L, the inflammation positivity rate of CSF cytology was significantly higher (68.3% versus 64.0%, p < 0.001).Conclusions The comparatively higher inflammation positivity rate and the superiority of evaluating cell morphology render CSF cytology an effective tool for identifying anti-NMDAR encephalitis and investigating its pathogenesis.