Objective To provide references to control the cost of stroke inpatients by analysing pertinent factors of stroke inpatients. Methods According to the models of Anderson and Newnan, univariable analysis and multivariable statistical analysis were applied to a number of factors including predisposing factors, enabling factors, and needs factors in 1 969 stroke inpatients of two third level first-class hospitals in Chongqing. Results Among the 1 969 stroke inpatients, 64% had a history of hypertension, and 50% exhibited hypertension during their stay in hospital. Expenditure on medication consumed the highest costs (51%). Length of stay was the most important factor affecting inpatient expense, additional factors were number of surgical operation, nurse type, Rankin score, number of complications etc. Conclusions Complex measures focusing on hypertension to prevent and control of stroke are recommended. Reducing unnecessary stay in hospital and appropriate prescribing are important methods to reduce cost of stroke inpatients.