ObjectiveThe low performance of primary medical institutions (PMIs) in China is a significant issue. The WHO proposed that the main reason for the failure of the healthcare system in developing countries is poor organisational capabilities. However, there is no international tool for evaluating the organisational capabilities of PMIs. Therefore, this study aimed to develop an index system for evaluating the organisational capabilities of PMIs.DesignWe searched the literature (English and Chinese) published before June 2020 in the PubMed, China National Knowledge Infrastructure and Wanfang databases to conduct a literature review and develop a preliminary indicator pool. Then, two rounds of Delphi expert consultations were conducted by email from June to September 2020, followed by screening, revision and supplementation of the indicators using the boundary value method. Finally, the analytic hierarchy process was used to determine the weight of the indicators.SettingThe Delphi consultation questionnaire was distributed to the leaders of PMIs in districts D, F and S in Beijing, China.ParticipantsNineteen leaders of PMIs who had a profound understanding of PMI operations and management and were able to participate in Delphi research from a professional and comprehensive perspective were included in this study.ResultsThe Cr values were 0.76 (first-level indicators) and 0.78 (second-level indicators), indicating that the expert consultation results were accurate and reliable. The result of the expert coordination coefficient test was significant at the p<0.01 level, suggesting that the experts’ views were consistent. The organisational capability index system includes 3 first-level indicators, 9 second-level indicators and 37 third-level indicators.ConclusionsAn index system for the organisational capabilities of PMIs was developed. This index system is a scoring system that focuses on basic service capabilities, management capabilities and sustainable development capabilities, and it can determine the priority of improvement areas for PMIs.