With the comprehensive harnessing the Yulin River in Chongqing, the harnessing model of the secondary rivers in Three Gorges Reservoir Area is discussed. It is believed that as for the comprehensive harnessing the water environment, the valley should be considered as a unit based on the whole ecosystem in the valley and the comprehensive consideration of the factors, influencing the ecology, resources, economy is needed in planning, protecting, improving and utilizing the water environment, in order to realize the sustainable development of the water environment in the valley. Moreover, the object, principles, measures of comprehensive harnessing the water environment in the valley were given.