OBJECTIVES: The prevalence of venous thromboembolism (VTE) has been increasing in China. However, the economic burden of the disease is not well understood. This study aims to estimate inpatient costs of VTE in China and identify key factors associated with costs. METHODS: Hospitalizations with a diagnosis of VTE (including deep vein thrombosis (DVT) or pulmonary embolism (PE)) were identified in a large hospital electronic medical record database that included 100% inpatient records from two tertiary hospitals between January 1^st, 2010 and June 30^th, 2013. Total costs per hospitalization as well as its components, pharmacy costs (all drug-related costs) and non-pharmacy costs (all other costs), were estimated using hospital billing data (in 2013 CNY) and converted to 2013 USD using an exchange rate of 6.12. Multivariate regressions were performed to assess factors associated with total hospitalization costs, including patient demographics, insurance status, VTE type, VTE diagnosis type, anticoagulant treatment, comorbidities, admission type, and surgical procedure. RESULTS: A total of 1,047 VTE-related hospitalizations were included in the analysis. The mean age at hospitalization was 62.4 years and 54.1% of hospitalizations occurred to men. DVT accounted for 77.1% of the total hospitalizations. The average pharmacy, non-pharmacy, and total costs per hospitalization were CNY 9,820 (USD 1,604), CNY 19,294 (USD 3,153), and CNY 29,114 (USD 4,757), respectively. Diagnosis of PE (vs. DVT), anticoagulant treatments (vs. no anticoagulant treatment), admission under critical condition, having surgical procedures, certain comorbidities, and VTE as secondary diagnosis were significantly associated with higher total costs per hospitalization (P < 0.05). CONCLUSIONS: In China, the inpatient costs of VTE are as high as 1.7 times of the average annual household income. Multiple factors, including VTE type, treatments, admission condition, etc., are associated with inpatient costs among VTE patients. Future studies are indicated to understand the cost variations.