To analyze the influencing factors and structural changes of the hospitalization Expenses for cerebral infarction in the county public hospital of Anhui Province. Methods: Medical and billing records of cerebral infarction patients who received treatments in 12 county public hospitals in Anhui from 2011 to 2015 were obtained, using descriptive analysis on the cost structure and the trend of the change in cerebral infarction patients, and using multiple linear regression analyze its influencing factors. Results: the number of hospitalizations，total cost of hospitalizations, average cost of hospitalizations, examination fees, materials fees and test fees were all increased; the average days of hospitalization and average proportion of medicine were decreased; The cost around northern southern and central part in Anhui is not balanced; the average days of hospitalization , gender, region, whether using the case-based payment and the clinical pathway as the main factors . Conclusion: Controlling the growth of the cost in patients with cerebral infarction,, we should reduce the incidence rate of cerebral infarction, optimize the cost structure in cerebral infarction, implement the clinical pathway and case-based payment reform, and so on.