There are divergent items in the free vibration solution of complex damping vibration equation. The structural free vibration responses cannot be calculated based on complex damping model, and the structural time domain calculation results are not stably convergent. On the basis of the complex damping model, the improved time domain motion equation can be obtained by time and frequency domain transformation. In the time step, it is assumed that the relationship of earthquake acceleration is linear. By the characteristics of the improved motion equation, the improved time domain calculation method under earthquake action is put forward. The cases show that， compared with the time domain motion equation of complex damping model, the improved time domain motion equation can be applied to the time domain calculation of structural free vibration responses. The structural time domain calculation results are stably convergent under earthquake action. Compared with the Fourier series method, the calculation amount of the proposed method is less and the computational efficiency of the proposed method is higher. With the increase of damping ratio, the difference between the improved time domain calculation method of complex damping model and the time domain calculation method of viscous damping model is increasing gradually. When the damping ratio is 0.5, the biggest relative error of structural acceleration peak values which are calculated by the two methods is over 20% under some seismic wave.