The invention discloses a method for predicting and evaluating strong earthquake resistance of a nuclear power station breakwater. The method includes the steps of firstly, building three-dimensional finite element models of the breakwater and a seabed foundation; secondly, performing working condition simulation on the earth and breakwater structure initial stress guided into the breakwater three-dimensional finite element model to obtain the initial stress state of the breakwater system; thirdly, adding external simulation conditions to the initial state breakwater system three-dimensional finite element model, and then using an explicit nonlinear finite element method to solve on a super computer platform to obtain the earthquake response of the breakwater; fourthly, evaluating the earthquake resistance of the breakwater according to the dynamic earthquake response of the breakwater system obtained in the third step. By the method, calculating efficiency and precision can be increased, design construction period of the breakwater can be shortened, and accurate and reasonable scientific guidance is provided with earthquake resistance design of the breakwater system and similar coasting defense projects.