Objective To change the deficiencies of the traditional performance evaluation model based on financial performance,give full play to the potential of hospital scientific research in the exploration of medical resources in hospital,improve the long-term development ability of hospital,and explore a new performance evaluation system of hospital scientific research.Methods By means of literature review combined with practice analysis,the paper conducted a comparative study on the advantages and characteristics of the research performance evaluation system and the traditional hospital performance evaluation system.Results The performance evaluation system of hospital scientific research based on balanced scorecard theory matches the dynamic process dimension of hospital scientific research.Conclusions The balanced scorecard-based performance evaluation system of hospital is able to change the previous rigid performance evaluation of scientific research,realized a dynamic and whole-process management mode which better mobilize the enthusiasm of medical staff for scientific research.