Purpose Long-term hospitalized patients with schizophrenia (SCZ) are vulnerable to physical illness, leading to impaired life expectancy and treatment outcomes. There are few studies on the influence of non-alcoholic fatty liver disease (NAFLD) in long-term hospitalized patients. This study aimed to investigate the prevalence of and influence factors for NAFLD in hospitalized patients with SCZ. Patients and Methods This cross-sectional retrospective study included 310 patients who had experienced long-term hospitalization for SCZ. NAFLD was diagnosed based on the results of abdominal ultrasonography. The T -test, Mann–Whitney U -test, correlation analysis, and logistic regression analysis were used to determine the influence factors for NAFLD. Results Among the 310 patients who had experienced long-term hospitalization for SCZ, the prevalence of NAFLD was 54.84%. Antipsychotic polypharmacy (APP), body mass index (BMI), hypertension, diabetes, total cholesterol (TC), apolipoprotein B (ApoB), aspartate aminotransferase (AST), alanine aminotransferase (ALT), triglycerides (TG), uric acid, blood glucose, gamma-glutamyl transpeptidase (GGT), high-density lipoprotein, neutrophil-to-lymphocyte ratio, and platelet-to-lymphocyte ratio significantly differed between the NAFLD and non-NAFLD groups (all P <0.05). Hypertension, diabetes, APP, BMI, TG, TC, AST, ApoB, ALT, and GGT were positively correlated with NAFLD (all P <0.05). The results of the logistic regression analysis indicated that APP, diabetes, BMI, ALT, and ApoB were the influence factors for NAFLD in patients with SCZ. Conclusion Our results suggest a high prevalence of NAFLD among patients hospitalized long-term due to severe SCZ symptoms. Moreover, a history of diabetes, APP, overweight/obese status, and increased levels of ALT and ApoB were identified as negative factors for NAFLD in these patients. These findings may provide a theoretical basis for the prevention and treatment of NAFLD in patients with SCZ and contribute to the development of novel targeted treatments.