Management system is a key factor on water quality protection and water pollution prevention in the drainage area. This paper elaborates the basic characteristic and connotation of drainage area management, analyzes the status quo and main problems of the existing management system of water quality protection in the Three Gorges Reservoir and its upstream areas, and compares the primary viewpoints and schemes of relevant government department on the reform of the management system. Then, it brings forward the structuring and tentative idea of water quality protection management system based on the conception of harmonious development of drainage area.