Taking account of soil-structure interaction on seismic wave input, based on the theory of a two-step method, equivalent seismic wave input considering radiation damping effects is established. Firstly, the base response of single degree of freedom system is considered as the input of superstructure; and then damping ratio of the system is calculated by the state-space method considering soil-structure interaction, which is used to modify the damping coefficients of superstructure; thus the impact of soil-structure interaction is approximately calculated from the response of rigid foundation. Subsequently, a single degree of freedom system and a five-story frame structure are analyzed; numerical examples show that the calculation errors even exceed 100%; while directly taking seismic wave of free field and bedrock as the input of superstructure. However, the calculation errors of the two-step method are less than 10%; furthermore, the calculation errors will be less than 5% adopting the modified damping two-step method, which can satisfy the requirements of engineering.