Objective To establish a cooperative decision-making model of county-level public hospitals, so as to freely select the best partner in different decision-making units and promote the optimal allocation of medical resources. Methods The input and output data of 10 adjacent county-level public hospitals in Henan province from 2017 to 2019 was selected. Based on the traditional data envelopment analysis (DEA) model, a generalized fuzzy DEA cooperative decision-making model with better applicability to fuzzy indicators and optional decision-making units was constructed. By inputting index information such as total number of employees, number of beds, annual outpatient and emergency volume, number of discharged patients, total income and hospital grade evaluation, the cooperation efficiency intervals of different hospitals were calculated to scientifically select the best partner in different decision-making units.Results After substituting the data of 10 county-level public hospitals in H1-H10 into the model, taking H2 hospital as an example to make cooperative decision, among the four hospitals in H1, H2, H7 and H10 of the same scale, under optimistic circumstances, the best partner of H2 hospital was H7 hospital, and the cooperation efficiency value was 1.97; in a pessimistic situation, the best partner of H2 hospital was H10 hospital, and the cooperation efficiency value was 0.98. The model had good applicability in the cooperative decision-making of county-level public hospitals. Conclusion The generalized fuzzy DEA model can better evaluate the cooperative decision-making analysis between county-level public hospitals.