Background: Apart from its direct impact on public health and well-being, malaria had placed significant socioeconomic burden on both individuals and whole health systems. This study was conducted to investigate the hospitalization cost of malaria and explore the inter-province variation during the National Malaria Elimination Programme in China. Methods: Information on medical expenditure for malaria treatment was extracted from inpatient medical records in Henan, Hainan and Guangxi Province. The costs were adjusted to the price in 2014 and converted to USD (United States Dollars). Non-parametric and parametric methods were employed to estimate hospitalization costs and nonparametric bootstrap method was used for the comparison of hospitalization costs among sample provinces and to estimate the uncertainty of differences in inter-province hospitalization costs. Results: The hospitalization cost and daily cost of 426 malaria inpatients were 929.8 USD and 143.12 USD respectively. The average length of stay was 11.95 days. The highest cost of hospitalization services occurred in tertiary hospitals (956 USD per episode). Whereas the lowest ones occurred in internal departments (424 USD). Medications, laboratory tests and supportive resources for treatment were the most important components of hospitalization costs, respectively responsible for 45.31, 24.70, and 20.09% of the total hospitalization costs. The hospitalization cost per episode in Henan Province was significantly higher than that in Hainan an in Guangxi Province, with incremental costs of 713 USD (95% confidence interval 419.70, 942.50) and of 735.58 USD (95% CI 606.50, 878.00), respectively. The differences in the daily costs between Henan and Hainan along with Guangxi provinces were 75.33 USD (95% CI 40.33, 96.67) and 93.56 USD (95% CI 83.58, 105.28), respectively. Conclusions: Although the prevalence of malaria cases has considerably declined, the direct hospitalization costs of malaria in the household remain high and the inter-province variations need to be seriously considered in the formulation the further interventions regarding hospitalization cost control. This study suggests that economic risk protection mechanisms targeting at malaria inpatients should be redesigned. The drug price addition policy in public hospitals should be gradually reformed or abolished coupling with increasing government subsidies along with the charges for treatment services to reduce the hospitalization cost. The policy for cost control in the provincial hospitals should be implemented in comparison with the policy in other provinces, where the status of economic and geography are similar.