Objective The development of scientific research performance in China's community health centers(CHCs) is in the initial phase.Moreover,there is lack of corresponding effective assessment systems.We aimed to develop a comprehensive scientific research performance assessment system for domestic CHCs,providing a reference for relative studies and assessments.Methods This study was conducted from March to December 2015.We determined the indicators in the comprehensive scientific research performance assessment system for CHCs based on systematic review of relative studies and Delphi expert consultation,and determined their weights by using analytic hierarchy process.Then,the validation of the assessment system was performed in 11 CHCs of Yangpu Hospital of Tongji University.Results Our assessment system consisted of 3 dimensions(scientific research input,scientific research output and scientific research management) and 23 indictors.The weighted consensus index for the indicators was less than 0.10.The validation and sensitivity analysis of the assessment system showed that,the ranking of 8 CHCs by the experts' objective assessment and by our study group using the assessment system(subjective ranking) differed less than 2.Conclusion The sensitivity and effectiveness of this assessment system proved its good feasibility.However,quality control and dynamic feedback are needed during large-scale data collection and analysis,so as to better support the development of scientific research performance in CHCs.