Hospitals need to explore based on their own specifics how to establish a modern hospital governance system and how a lean hospital administration level be achieved. This paper introduced the practice and exploration of modern hospital governance system construction in Beijing Tsinghua Changgung Hospital as follows. The hospital is run by a board of administration featuring co-administration by both Beijing Municipal Hospital Administration Center and Tsinghua University; A hospital charter is developed and agreed upon to regulate decision-making, day-to-day operations and supervision; The hospital president′s responsibility is under the leadership of the hospital′s Communist Party Committee; Benefiting from best practices of Taiwan Changgung′s medical system, the hospital′s specialized medical teams and professional administrative teams operate in cooperative governance, and under professional management model and a lean operation management system. The practice and exploration of Beijing Tsinghua Changgung Hospital can serve as references for building and perfecting a modern hospital governance system.