A nonlinear dynamic coupled model for hydropower station system, which contains the model of water-carriage system, water turbine system, speed governor system, generator's electromagnetic system, grid, shaft system of hydroelectric generating set, as well as the powerhouse, is established in this paper. Firstly, the simultaneous differential equations for coupled hydraulic-mechanical-electric transient process are set up based upon the theories of hydraulics, electrical machinery, etc., while the coupled structural models for shaft system of unit and powerhouse are built by means of finite element method. Secondly, a new method for investigating nonlinear dynamic properties of structures influenced by coupled hydraulic-mechanical-electric factors in different conditions is introduced with the help of user-programmable features from Ansys software. Finally, in order to verify the rationality, several numerical calculation methods are used to study the starting-up process of hydropower station. The results indicate that the model presented in this paper is adoptable for simulating specified condition and reflect the nonlinear dynamic characteristics of hydropower station comprehensively. In addition, the model can also be used to assess the operation safety and predict the structures reliability of hydropower station system, so as to provide some profitable reference for dynamic regulation during limited and transient conditions for hydropower station.