Soil flexibility has an obvious effect on damage for buildings during past seismic events. When a structure is subjected to earthquake, its foundation undergoes three modes of deformation, namely vertical, sliding, and rocking. Indeed, the present practice of structural design assumes that buildings are fixed at their base as the connection between columns and foundation. However, in reality, the supporting soil flexibility especially, under the raft foundation system permits extra lateral deformation to their natural deformation. So, implementing soil-structure interaction (SSI) modeling enables the designer to assess the actual inelastic seismic performance and the base shear capacity of the structural system. In this study, three-dimensional finite element (FE) models of multi-story moderate-rise buildings are constructed by ETABS to analyze the effects of soil flexibility underneath raft foundation on the inelastic seismic performance via performance based seismic design (PBSD) concept. Numerical results are obtained using Winkler model spring for soil-structure interaction's simulation in both vertical and horizontal directions. Comparison is carried out between different methods of soil subgrade modulus calculation such as FEMA, NIST, and ECP-202. Also, various soil types are included and compared to those corresponding to fixed-base support. The findings demonstrate that numerical models under flexible (soft) soil and ECP-202 equation of soil subgrade modulus have extra time period, lateral deformation, and inter-story drift than that with fixed base. Also, the capacity curve, global ductility ratio, plastic hinge formation, and performance point have evident variation as a result of SSI.