Considering the coupling effect between fluid phase and solid phase, the site soil on bedrock is considered as two-phase saturated porous media. In order to consider the viscoelastic characteristics of the saturated site soil, the stress-strain relationship of soil skeleton is described by fractional derivative Kelvin viscoelastic model, and the motion control equations of overlying fractional derivative viscoelastic saturated site soil under the action of harmonic earthquake wave are established. Using the properties of fractional derivative and considering the boundary conditions and permeable conditions, the vibration problem of overlying fractional derivative viscoelastic saturated site soil under the action of harmonic earthquake wave is solved, and the seismic displacement amplification coefficient of the saturated site soil is also obtained. The influences of the order of fractional derivative, liquid and solid coupling coefficient, model parameters of soil, and bedrock and soil shear modulus ratio on the seismic displacement amplification coefficient are analyzed and discussed by numerical examples. The results show that the order of fractional derivative, liquid and coupling coefficient, model parameters of soil, bedrock and soil shear modulus ratio have great effects on the seismic response of the site soil. The fluid and solid coupling coefficient could the increa of be increased and the seismic response can be decreased by compacting the saturated soil. Meanwhile, the viscosity and shear modulus of the saturated site soil can also reduce the seismic response.