Abstract: The construction of water conservancy and hydropower brings about the enormous economic and social benefits, but meanwhile it also changes the hydrology of original-river wetland ecosystems drastically. We built dams blocking the river, which has caused a series of circumstances, such as habitat fragmentation and so on. These conditions have had a significant impact on wetland ecosystems. How to protect in the process of development and how to develop in process of protection are the key issues that we must pay more attention and address in the construction of hydropower projects. Based on the observation data of water and sediment prototype, a onedimensional hydrological and hydrodynamic model was built. We studied the hydrological changes in the process of power plant construction, and simulated changes of the flow state under different situations. On this basis, combining two-dimensional hydrological and hydrodynamic model, we conducted the fine simulation of the flow structure of key rivers where typical wetlands and fish spawning grounds exist. Moreover, we also analyzed the impact of hydropower development on changes of the water level, water depth, flow field, etc., researching on habitat condition changes caused by it. Based on the above achievements, the paper puts forward a series of engineering measures including discharge of ecological flow, protection and construction of important fish habitats, river ecological restoration, node protection of important wetlands and typical design restoration.