Objective To analyze the spatial distribution characteristics and operational efficiency of resources of Guangxi private hospitals, so as to provide empirical evidence for improving the input⁃output efficiency of Guangxi private hospitals and optimizing the allocation of medical resources. Methods A total of 80 Guangxi private hospitals were selected as sample hospitals. The geographic information system and three⁃stage data envelopment analysis (DEA) model were employed to perform spatial distribution characteristics analysis and efficiency evaluation on resources of Guangxi private hospitals. Results (1) Before the adjustment, the average values of comprehensive efficiency, pure technical efficiency and scale efficiency among the 80 sample hospitals were 0.608, 0.785 and 0.762, respectively, therein 14 sample hospitals achieved overall effectiveness and scale effectiveness, and 27 sample hospitals achieved technical effectiveness. (2) Before the three⁃stage DEA adjustment, the average value of pure technical efficiency of the sample hospitals was higher than that of scale efficiency. After excluding the influence of environmental factors, the average values of comprehensive efficiency and pure technical efficiency of the sample hospitals increased, and the number of sample hospitals achieving technical effectiveness increased to 31, while the average value of scale efficiency decreased. (3) Before and after the adjustment, 66 sample hospitals failed to achieve overall effectiveness and scale effectiveness, and 52 sample hospitals had increasing returns to scale, while 14 hospitals had decreasing returns to scale. (4) In terms of hospital types, after the adjustment, the average values of various efficiency of ophthalmology hospital, general hospital, orthopedic hospital, rehabilitation hospital and maternity hospital changed little as compared with before the adjustment; furthermore, the average value of pure technical efficiency of hospital for Traditional Chinese Medicine increased significantly, while that of psychiatric hospital decreased significantly. (5) In terms of regions, after the adjustment, the pure technical efficiency of sample hospitals in Baise increased by two echelons. The comprehensive efficiency and scale efficiency of Baise sample hospitals, the comprehensive efficiency, pure technical efficiency of Nanning sample hospitals, and the comprehensive efficiency, pure technical efficiency, and scale efficiency of Liuzhou sample hospitals, as well as pure technical efficiency of Hezhou sample hospitals all increased by one echelon, while only the scale efficiency of Yulin sample hospitals decreased by one echelon. Conclusion The development of Guangxi private hospitals is uneven. There are differences in resource distribution and operational efficiency among different types and regions of private hospitals. Scale efficiency and technical management level need to be improved, therein environmental factor exerts a significant effect. It is suggested that Guangxi private hospitals should be patient⁃oriented, rationally allocate medical resources, improve technical management level, enhance operation quality and efficiency, and achieve scale economy and characteristic development; simultaneously, relevant health administrative departments should optimize the external environment for the development of private hospitals, and promote the high⁃quality development of private hospitals in Guangxi.