This study presents a framework to perform Probabilistic Seismic Hazard Analysis (PSHA) for soil sites, which yields accurate soil UHS and associated seismic hazard curves. The variabilities of soil parameters, the nonlinear responses of soils, and the vector-valued site responses analysis comprehensively integrate into the PSHA for soil sites. In this framework, site amplification is used to modify the Ground Motion Prediction Equations (GMPEs) to make them suitable for a soil site. Based on the modified GMPEs with updated uncertainties, PSHA for soil sites are performed accurately; thus, acceptable soil UHS and associated seismic hazard curves considering site-specific uncertainties could be achieved. Using an example soil site, influences of soil parameter variabilities and soil nonlinearity on UHS and associated seismic hazard curves are discussed in this study.