Objective To evaluate and follow-up the cognitive function during convalescence of anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis in children in southern China. Methods The clinical data of children with anti-NMDAR encephalitis diagnosed and treated from 2016 to 2021 were retrospectively analyzed. According to the modified Rankin Scale (mRS Score) in the acute stage, the patients were divided into the severe group (mRS>3) and the non-severe group (mRS≤3). The results of Wechsler intelligence scale at the acute stage discharged from hospital and last follow-up were collected and analyzed. Results A total of 33 children (15 boys and 18 girls) were included in the analysis. The age of first onset was 6.0 (5.0~9.0) years. The clinical features in the acute stage were mainly convulsion (n=31), psycho behavioral symptoms (n=28), and movement disorder (n=28). The time from discharge to the last follow-up was 12.0 (4.0-33.0) months. At the last follow-up, the mRS Score was 0.0 (0.0~0.0), the full-scale intelligence quotient (FSIQ) was 82.4±12.1, the verbal comprehension index (VCI) was 85.6±16.7, the working memory index (WMI) was 84.7±13.5, and the processing speed index (PSI) was 83.5±11.0. The FSIQ and subtests scores of the children were lower than the normal level. No statistically significant differences was found in FSIQ and subtests between the severe group and the non-severe group (P>0.05) at the last follow-up. Ten children received two Wechsler intelligence tests. The time of the first test was 3.0 (1.0-5.7) months after the discharge of the first onset, and the time of the second test was 21.0 (15.5-28.0) months after the discharge of the first onset. FSIQ and VCI of the second test were higher than those of the first test, and the difference was statistically significant (P<0.05). Conclusions Children with anti-NMDAR encephalitis have cognitive impairment in the convalescence period. It is recommended to conduct regular intelligence assessment and timely reasonable intervention.