Objective: Taking schizophrenia as an example, the paper explores the influencing factors of inpatient bed-day based expenses in patients with mental disorders to provide the reference for controlling irrational increase of medical expenses and improving medical quality, and to provide theoretical basis for the implementation of bed-day based payment methods in mental institutions. Methods: Single factor analysis and multiple linear regression analysis were used to collect medical insurance settlement data of Shanghai employee medical insurance patients with schizophrenia in 2021 for analysis. Results: A total of 11774 patients' information was included, with a median inpatient bed-day based expenses of 403.93 yuan. The age, gender, institutional level, institutional nature, presence or absence of comorbidities, presence or absence of surgery, length of hospital stay, and disease type of the included patients have significant impact on inpatient bed-day based expenses. Conclusion: The inpatient bed-day based expenses of patients with mental illness are affected by multiple factors. When formulating the payment method for medical insurance of mental illness, multiple factors need to be considered in order to achieve the goals of cost control, quality improvement, and efficiency enhancement.