Identification of system parameters of structures is important for the damage detection or health monitoring of structures due to earthquake. Generally, the input and responses of structure is measured by the accelerometers during earthquake. Therefore, if it is possible to identify the system parameters by wavelet transform of input and acceleration response, it is very useful. In this paper, the method to identify the system parameters such as stiffness matrix and damping matrix by wavelet transform of input and acceleration records observed during earthquake is proposed. To verify the applicability of the proposed method, numerical simulations using the two-degree-of freedom system and the experimental using two story model are conducted. From both results, it is proven that the proposed method can give the good estimation for the system parameters compared with the other methods.