Objective To compare and analyze the clinical skill score of 20 866 candidates from 9 provinces (autonomous regions and municipalities) in 2016 China pilot medical licensing examination for rural assistant general physicians, learn from the analysis and further improve the examination.Methods Passing rate, rate of correct answer and mean score are applied in comparison and analysis.Results Passing rate is related to gender, nationality, district, education and career background. Routine physical examinations and operations are best observed, while basic knowledge needs to be improved.Conclusions The result of examination data analysis verifies the scientificity and rationality of the examination design, and lays the foundation for the formal implementation of the examination. It also provides a reference for the decision-making department to further strengthen the construction of primary medical and health teams.