OBJECTIVE： To establish hospital pharmacoeconomic evaluation system by cost-effectiveness analysis and decision tree algorithm. METHODS： Through the exploration and analysis of cost-effectiveness analysis method， hospital pharmacoeconomic evaluation system was constructed by decision tree algorithm； the design process， overall framework， application functions and application examples （Atorvastatin calcium tablet vs. Rosuvastatin calcium tablet） of the system were introduced. RESULTS： The established hospital pharmacoeconomic evaluation system was used to extract， analyze and integrate the data such as drug cost， treatment effect. The decision tree algorithm is used to deal with the results. Finally， the results of pharmacoeconomic evaluation are shown to users in a graphic way. The overall framework of the system mainly includes the hospital business platform， the data integration platform， the information processing platform and application service platform； the application functions include drug cost-effectiveness analysis， drug incremental cost-effectiveness analysis and sensitivity analysis of evaluation results. The example analysis showed that expected cost-effectiveness ratio of Rosuvastatin calcium tablet were 6 644.44 yuan； that of Atorvastatin calcium tablet was 6 926.63 yuan； incremental expected cost-effectiveness ratio of Atorvastatin calcium tablet was 117 579.17 yuan. The sensitivity analysis conclusion was consistent with the cost-effectiveness analysis conclusion. CONCLUSIONS： The established system solves the problems during the development of pharmacoeconomic evaluation， such as “difficulty in cost-effectiveness data collection” “uniform calculation method” “lack of sensitivity analysis for evaluation results”， which can improve the level of rational drug use in hospital.