The digital economy has penetrated various fields of the social economy, including the healthcare industry, and the high-quality development of hospitals requires high-quality middle-level managers. Most middle-level managers in Chinese university affiliated hospitals come from medical technology backbones, and the phenomenon of “double shoulders” is common. They are tired of coping and lack professional knowledge in management. Constructing a scientific competency model for middle-level managers in Chinese university affiliated hospitals is not only a reference for cultivating middle-level managers in Chinese university affiliated hospitals, but also of great significance for improving the quality of middle-level managers in Chinese university affiliated hospitals. The article extracts the competence qualities of middle-level managers in Chinese university affiliated hospitals through literature analysis and grounded theory and uses fuzzy analytic hierarchy process to determine the weights of various elements of competence, constructing a competence model for middle-level managers. The results show that the competency qualities of middle-level managers in Chinese university affiliated hospitals can be summarized into 26 competency qualities, including five dimensions: digital technology ability, hospital decision-making ability, hospital management ability, personal characteristics, and knowledge learning ability. Among them, hospital management ability and decision-making ability are the most important dimensions.