Due to the influence of many factors in the actual seismic acquisition process such as the low frequency noise, initial velocity and acceleration, and human operation error, serious baseline drift occurs in the seismic wave displacement time history curve. Therefore, the acceleration record needs to be corrected in the process of structure earthquake response analysis. Based on the method of Iwan and EMD, a new method is proposed to deal with the baseline drift of seismic wave. The new method retained the characteristics of initial record, such as acceleration peak and frequency features, and can remove the baseline drifts of velocity and displacement curves. The seismic dynamic response of the earthquake was calculated using the ANSYS combined with “large mass method” and “displacement method” based on the new method mentioned above. The results showed that the baseline drift processing method proposed in this paper can ensure the correction of the baseline drift of seismic waves better without changing the peak and spectrum characteristics of the original records. The research results have guiding significance for filtering bleaching phenomenon caused by low frequency noise, initial value and artificial operation error.