A Fourier series non-stationary coherency model with respect to the site conditions for the horizontal component was developed. The evolution of the model was achieved using parameters related to the site, interstation distance, and time. First, based on the simulation of a non-stationary ground-motion field considering the wave-passage effect and site-response effect, the approach used for the estimation of coherency using wavelet transform is presented. Subsequently, the Fourier series non-stationary coherency model is formulated. The parameters are considered piecewise constant variables to represent the non-stationarity of the estimated coherency. The entire non-stationary strong ground motion was divided into ten parts according to the cumulative energy. The effects of the site and inter-station distance on the proposed model are presented. Parameters related to the site and interstation distance were obtained. Finally, the proposed model is compared with the ground motion records at the SMART-1 array during Event 45, the stationary model, and the data from the Argostoli rock site dense array. This indicates that the Fourier series non-stationary coherency model with respect to site conditions for the horizontal component can well match the correlation of the realistic spatially variable seismic ground motion, which is related to the site, time, and inter-station distance.