Reservoir regulation process in the Yangtze River basin is mainly divided into two types of flood regulation and initiating benefit regulation. The present reservoir management system and operation mode are mainly for dealing with or coordinating of flood control and benefit initiation as well as benefit distribution among various beneficial functions. From the view point of river ecosystem protection, the current regulation mode has two kinds of problems: firstly, most of the reservoir regulation plans do not consider ecosystem protection at downstream of dams and needs of environment protection in reservoir areas; secondly, integrated regulation or management of water resources is ignored. It is very necessary to improve reservoir regulation mode, bearing problems faced by regulation of the Three Gorges reservoir and issues related to cascade development and regulation in Tuojiang and Minjiang River basins in mind. In accordance with the concept of scientific development, and the philosophy of “ensuring a healthy Yangtze River and promoting the harmony between human and water”, taking flood control, benefit initiation and ecosystem as a whole, this paper put forward the basic consideration to improve reservoir regulation as follows: on the basis of requirements of ecosystem protection at downstream of dams and needs of environment protection in reservoir areas, we should bring the functions of reservoir such as flood control and benefit initiation into full play, control the negative influence to the ecosystem at downstream of dams and the environment in reservoir areas in an endurable scope, and restore the ecosystem and the environment step by step. This paper put forward the relevant regulation process aiming at the idiographic problems such as protection of ecosystem at downstream of dams and environment in reservoir areas, protection of aquatic wildlife species and fish species, regulation of sediment and protection of wetland.