For general engineering structure, the low order modes play a leading role in the structural dynamic response. In order to avoid an arbitrary selection of two reference vibration modes used to evaluate the two coefficients of Rayleigh damping, a formulation of optimizing Rayleigh damping coefficients based on the fundamental frequency of structure was developed. Based on the empirical equation of earthquake spectrum varying with damping ratio, the approximate solution on the derivation of response spectrum was obtained. Therefore, a formulation which includes the comprehensive effects of structural dynamic characteristics and frequency content of seismic excitation was addressed. Seismic responses of a free field subjected to 10 earthquake waves were analyzed, different Rayleigh methods were discussed, and the effectiveness of the proposed method was demonstrated.