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Background: To promote the integration of medical resources, Beijing has built medical alliances since 2012, but this reform has not changed the state of disordered medical treatment. Patients are still willing to go to high-level hospitals for medical treatment. What causes patients to prefer high-level hospitals? To explore the reasons behind this preference for high-level medical treatment among patients and to guide patients to make visits in an orderly manner, we conducted this study and compared patients' satisfaction with hospitals of different levels in the context of medical resource integration.Methods: This study conducted a questionnaire survey among 1250 patients who were selected in 18 medical alliances in Beijing from October to December 2016. The study type is a comparative study based on cross-sectional data. Patient satisfaction was the main outcome, and descriptive analysis, chi-square tests, nonparametric tests and binary logistic regression analysis were used. The level of statistical significance was set at p < 0.05.Results: The overall satisfaction score of the medical alliances was 3.375, and the satisfaction scores of core hospitals and cooperative hospitals were 2.77 and 3.07, respectively. The overall patient satisfaction rate was 44.62%, and the satisfaction rates of core hospitals and cooperative hospitals were 34.34 and 50.43%, respectively. The type of hospital and understanding of medical alliance policy were the factors associated with patient satisfaction with the medical alliance.Conclusions: The patients' satisfaction with cooperative hospitals was higher than their satisfaction with core hospitals. Although the patients were more satisfied with the service attitude of the cooperative hospitals, they still preferred core hospitals due to their higher expectations for their medical treatment and greater trust in their medical technology. It is necessary to explore the establishment of closed medical alliances under the unified management of human and financial resources to enable medical alliances to become a community of common interests and provide integrated medical services for patients. [ABSTRACT FROM AUTHOR]