To analyze the effects of Rayleigh damping coefficients reference frequency selection method on structural seismic response, some methods to estimate Rayleigh damping coefficients including the frequency contents-based second reference frequency, IDRISS method, traditional method and the optimization method were compared by the errors of top displacement and base shear with a 85.2 m length, 61.8 m width reticulated shell. As for the frequency contents of earthquake waves, the statistics ranges of the peak and centroid frequencies of pseudo-acceleration-, pseudo-velocity-and displacement response spectrum were discussed. The numerical results show that: the second reference frequency specified by the peak and centroid frequencies of the pseudo-velocity-and displacement response spectrum as well as peak frequency of the Fourier spectrum make the response results smaller than the exact ones. The estimation error is reasonable, which the second reference frequency is equal to the peak and centroid frequencies of the pseudo-acceleration response spectrum in the range below the fundamental frequency. It is suitable that the reference frequency is estimated by the smoothing peak frequency of the Fourier spectrum in the IDRISS method when the predominant frequency of earthquake wave is greater than the fundamental frequency of structure. Optimization method can get the Rayleigh damping coefficient directly, eliminate the arbitrariness of reference frequency and have high calculation accuracy.