Objective To investigate the correlation of low triiodothyronine (T3) syndrome with the severity and prognosis of patients with anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis. Methods The clinical data of 32 patients with anti-NMDAR encephalitis diagnosed in The First Affiliated Hospital of Naval Medical University (Second Military Medical University) from Jan. 2016 to Jan. 2021 were retrospectively analyzed. According to the serum free triiodothyronine (FT3) level measured for the first time after admission, the patients were divided into low T3 syndrome group and normal thyroid function group, and the demographic information and clinical characteristics of the 2 groups were compared. According to the modified Rankin scale (mRS) score at 2-4 weeks after onset, the patients were divided into good prognosis group (mRS＜3) and poor prognosis group (mRS≥3), and the clinical characteristics and laboratory findings of the 2 groups were compared. Pearson bivariate correlation analysis was used to explore the correlation of low T3 syndrome with the severity and prognosis of anti-NMDAR encephalitis. Results Among the 32 patients, 14 (43.75%) had low T3 syndrome. Compared with the patients in the normal thyroid function group, the patients in the low T3 syndrome group had higher incidence of consciousness disorder, higher mRS score at admission, higher rates of epilepsy and pulmonary infection, higher abnormal rate of cranial magnetic resonance imaging, and higher mortality (all P＜0.05). The proportions of patients with poor prognosis combined with low T3 syndrome, status epilepticus, fever, or pulmonary infection were higher than those of patients with good prognosis (all P＜0.05). Correlation analysis showed that FT3 level was negatively correlated with mRS scores (r＝－0.514，P＝0.003). Conclusion The change of thyroid hormone levels in patients with anti-NMDAR encephalitis may be related to the self-protection in vivo, and may be a potential biomarker of poor prognosis in patients with severe anti-NMDAR encephalitis. Routine monitoring of FT3 level has important clinical significance in risk stratification and prognosis prediction of anti-NMDAR encephalitis patients.