Evaluating the governance capacity of urban public health is the key to improving the level of urban public health. We aimed to evaluate the governance ability of urban public health. An index system of governance ability of urban public health was established. The governance ability of urban public health was evaluated, and major constraints against the ability improvement were analyzed through the EM (Entropy Method)-AHP (Analytic Hierarchy Process)-TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) model and data of urban agglomeration in Yangtze River Delta, China in 2023. Shanghai, Nanjing, Hangzhou, Suzhou, and Ningbo rank top 5 in terms of governance ability of public health, and they are in the first echelon. Hefei, Yancheng, Wuxi, Taizhou and Shaoxing rank 6-10, and they are in the second echelon. The remaining 17 cities are in the third echelon. Major sources of governance ability of urban public health and major factors that decrease governance ability are Medical Facility (A12), Health Improvement (A33), Medical Staff (A13), Government Ability (A11), and Health Loss (A34). For urban agglomeration in Yangtze River Delta, China, public health foundations, environmental exposure risks, public health performance, and public health emergencies all can influence the governance ability of public health. Accurate evaluation of the governance ability of urban public health can provide guidance and policy propositions to improve the governance system of public health and improve the emergency coordination ability of the government.