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Objective To explore the factors influencing the severity of acute phase and short-term prognosis of anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis, and search for potential indicators for assessing disease severity and predicting prognosis. Methods A total of 60 patients with anti-NMDAR encephalitis admitted to West China Hospital, Sichuan University from January 2020 to July 2023 were included. According to the modified Rankin Scale (mRS) during the acute phase, they were divided into mild group (mRS ≤ 3 score, n = 25) and severe group (mRS > 3 score, n = 35), as well as good outcome group (mRS ≤ 3 score, n = 32) and poor outcome group (mRS > 3 score, n = 28) based on the mRS score after one month of treatment at our hospital. Univariate and multivariate Logistic regression analyses were used to determine the risk factors of anti-NMDAR encephalitis with severe condition during the acute phase and poor short - term prognosis. Results Logistic regression analysis showed consciousness disorder (OR = 8.975, 95%CI: 2.048-39.327; P = 0.004) and high level of neutrophil percentage-to-albumin ratio (NPAR; OR = 5.004, 95%CI: 1.138-22.011, P = 0.033) were the risk factors of anti-NMDAR encephalitis with severe condition during the acute phase, while high level of serum IgE was the protective factor (OR = 0.994, 95%CI: 0.989-0.999; P = 0.026). Female (OR = 4.380, 95%CI: 1.205-15.929; P = 0.025), consciousness disorder (OR = 5.493, 95%CI: 1.535-19.657; P = 0.009) and high level of NPAR (OR = 2.949, 95%CI:1.010-8.612; P = 0.048) were the risk factors of anti-NMDAR encephalitis with poor short-term prognosis. Conclusions Consciousness disorder, low serum IgE level and high NPAR are risk factors of anti-NMDAR encephalitis with severe condition during the acute phase, while female, consciousness disorder and high NPAR are risk factors of anti-NMDAR encephalitis with poor short-term prognosis. NPAR is a potential biological indicator for assessing disease severity during the acute phase and predicting short-term prognosis of patients with anti-NMDAR encephalitis.