This study aims at presenting a new framework for probabilistic seismic hazard analysis with focus on Fourier amplitude and group delay time to calculate ground motion time histories corresponding to target annual probability of exceedence, considering source, path and site amplification effects especially due to deep subsurface profiles. Instead of depending on ground motion indices such as peak acceleration or acceleration response spectrum, the present method makes use of the linear operation among source, path and site effects on Fourier amplitude spectra, and directly calculates ground motion time histories with the stochastic Green's function method. In this paper, in addition to the methodology, an application of the method to the sites in Kanto region is illustrated.