Abstract: Objective In order to promote the development of the discipline, the scientific evaluation method is used to screen the evaluation indicators of the competence of clinical leaders. An objective and accurate evaluation system for competency is established and applied to the evaluation, training and selection of clinical leaders. Methods This study used Delphi method to conduct a round of questionnaire survey of 35 experts, and the analytic hierarchy process to establish the hierarchical structure of the competency evaluation index of clinical discipline leaders, constructed a pairwise comparison judgment matrix and determined the index weight and conduct consistency test. Results The constructed indicators include 5 first-level indicators, 19 second-level indicators, and 27 third-level indicators. The indicator design is updated in the human resource management platform to realize real-time data update and strengthen the operability of statistics. Conclusion An effective competency evaluation system is set up and reflects the hospital's emphasis on clinical skills, research performance and subject development, and clarifies the core competencies that clinical discipline leaders should possess, and will appoint, evaluate, manage and train clinical patients in the future. Academic leaders provide a scientific and rational basis for quantification.