Through on-site large-scale shaking table tests, the transfer function theory is used to derive the relative transfer function and the absolute transfer function, and these two transfer functions are compared with regard to their characteristics and the adopted dynamic parameters, and then the feasibility and accuracy for estimating the frequency domain response are analyzed. It is shown that the imaginary parts of the two transfer functions are equal to each other, and the dynamic parameters estimated by using the imaginary part of the two transfer functions are the same. The imaginary part of the two transfer functions and the module of the relative transfer function can be used to calculate the natural frequency of site, while the imaginary part of the two transfer functions and the module of the absolute transfer function are suitable for the calculation of the damping ratio. The acceleration vibration modes calculated by the real part, imaginary part and module of the two transfer functions are the same. It is feasible to estimate the seismic response of site in the frequency domain by the transfer function and the relative transfer function yields better results than the absolute transfer function.