Medication is critical in schizophrenia therapy, and prescription patterns have changed considerably over the past 20 years in China. This study attempts to evaluate the prescription patterns of antipsychotics for inpatients with schizophrenia in China and to identify factors influencing these patterns. Claims data of inpatients diagnosed with schizophrenia in 2010 were derived from the reimbursement database of Wuhan and Wuxi. A total of 5251 inpatients received antipsychotic medications, of whom 29.0% received second-generation antipsychotics apart from clozapine (SGAs#), 13.7% received clozapine (CLO), 13.5% received first-generation antipsychotics (FGAs), 43.8% received at least both drug classes, and 5.1% used FGAs, CLO as well as SGAs#. Multinomial logistic regression for 2904 identified inpatients showed that factors of drug reimbursement policy, duration of hospitalization, age group, and municipality were statistically significant in antipsychotic medication. Drug list B and the 25–45 age group presented a significant relationship with SGAs# prescription (FGAs vs. SGAs#). Furthermore, the 12–30-day duration of hospitalization and the 25–45 age group showed a significant relationship with SGAs# prescription (CLO vs. SGAs#). Socioeconomic factors such as health insurance policies, especially reimbursement policy of drugs and payment system, as well as mental health resource distribution are important in antipsychotic prescription in China.