Soil flexibility had an obvious effect on damage of 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 a simulation of 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 base shear capacity of the structural system during seismic event. In this study, three-dimensional finite element (FE) models of multi-story moderate-rise buildings of moment resisting frame (MRF) are idealized using ETABS to analyze the effects of soil flexibility underneath raft foundation on the performance based seismic design (PBSD). Winkler model spring is used for soil-structure interaction’s simulation in both vertical and horizontal directions. Comparison is carried out between different methods of soil subgrade modulus’s calculation such as FEMA, NIST, and ECP-202. Also, the results obtained for models with various soil types, and raft thickness are compared to those corresponding to fixed-base support. The findings demonstrate that numerical models using flexible (soft) soil, using ECP-202 equations, or less raft thickness have extra time period, lateral deformation, and inter-story drift (ISD) than that with fixed base or even with stiff soil. Also, the capacity curve, global ductility ratio, overstrength ratio, and damage index have evident variation of inelastic seismic performance as a result of SSI.