The design of earthquake resistant structures founded on combined piled raft foundation (CPRF) mainly depends on raft-pile-soil interaction (RPSI). This interaction become more complex for these heavy structures, if founded on the liquefiable soil. The CPRF is considered to be useful foundation in practice to support such heavy structure; in which both raft and pile increase the bearing capacity of the soil. Where raft reduces the liquefaction induced settlement and piles help to transfer the load of the structure to the non-liquefiable soil layer. The aim of this paper is to carry out the 3D nonlinear finite difference analysis of CPRF considering the RPSI. A recently developed constitutive model i.e. CycLiq for the liquefaction modelling of the soil is utilized to represent the behaviour of sand in inelastic range which consider the cyclic behaviour and large post-liquefaction shear deformation of sand. The validation of the model is carried out with the centrifuge data. The effect of CPRF over the raft and pile group is carried out for harmonic excitation with varying frequency and earthquake motion with varying PGA. The study provides important observations and insights that were not previously evident. The findings emphasize the need to consider frequency effects, geometrical nonlinearity, and material nonlinearity in the design of NPP structures. Additionally, the study introduces the application of the CycLiq liquefaction model and the development of a user-defined material for FLAC3D. Further, the outcome shows the useful conclusion on the importance of CPRF foundation over the conventional foundation i.e. raft and pile group in the liquefiable soil. It is found that excitation frequency, ground motion PGA, porosity of sand and pile spacing of CPRF have great effects on the response.