The reasonable and effective seismic wave input method is the key for the soil-structure dynamic interaction analysis. A new seismic wave input method based on the internal substructure is proposed based on the theory of wave method,in which the equivalent input seismic loads are directly obtained from the dynamic analysis of the internal substructure intercepted from the computational model. By doing so,the free wave field and the scattered wave field are separated,and the external seismic wave input problem is transformed into the internal wave problem of the calculation domain. The proposed wave input method effectively improves the efficiency of the equivalent input seismic load calculation and the seismic wave input. On the other hand,it avoids the participation of artificial boundaries in the process of inputting seismic waves. Thus the limitations on the type of artificial boundaries are completely reduced,which makes this method be able to be adopted more universally. In addition,the implementation steps of the proposed wave input method in the soil-structure dynamic interaction analysis are introduced in detail . The effectiveness of this new method is verified through the numerical examples of the free wave field and the soil-structure interaction system under obliquely incident waves.