ObjectiveTo explore the comprehensive hospital administrative management system for urban and rural cooperation in the process of medical reform. MethodsBy reviewing literature and interviewing directors of the administrative departments and hospital medical staff, we gradually established and improved the administrative management system for urban and rural hospital counterpart support. ResultsBetween 2010 and 2013, 123 medical workers were dispatched to support eight county-level hospitals, after which the comprehensive capacity, and technology and quality control in those hospitals were largely improved. Till the end of 2013, two of those hospitals were promoted to be grade-three class-B comprehensive hospitals; two were promoted as grade-two class-A comprehensive hospitals; three passed the reassessment to be grade-two class-A comprehensive hospitals; and another three county-level medical centers were promoted to be city-level key disciplines. ConclusionThe comprehensive administrative management system improves the management level of grass-roots hospitals at the county level; promotes the social public welfare of tertiary public hospital counterpart support; facilitates the process of medical system reform at the county level; establishes a series of administrative management modes such as unified support, personnel management, assessment standards and evaluation system; and promotes the sustainability of long-term counterpart support system.