The coupling of hydralic model and physical habitat model is used to demonstrate the response relation between hydraulics and biological life process in Xin'An River, and also to explore the optimal habitat of aquatic organisms and provide the gist in establishing a system theory. Based on the model of physical habitat, the paper simulated the water depth and flow distribution of Xin'An River under different flow conditions by MIKE 21-two-dimensional hydraulic model. The curve of flow -WUA is drawed by PHABSIM model, which shows that the appropriate ecological flow of rainbow trout is 160 m3/s. The value is between very good and the best line. The calculated result is reasonable and can provide reference for the protection of rainbow trout and the ecological scheduling of Xin'An river reservoir.