<p>Piled raft foundation system was first implemented in Mexico City 60&#xa0;years ago and has since been used in various buildings and skyscrapers, such as the Messeturm building, the Torhaus building, and the Westend 1 tower. Previous research has investigated the behavior of piled raft foundation under vertical loads, where the differential settlement control approach is the most commonly adopted approach. However, the behavior of piled raft foundations under seismic excitations and horizontal loading requires further extensive studies. Initially, this study uses numerical modeling with PLAXIS 3D software, incorporating necessary simplifications, to verify the results against previous centrifuge tests. Based on the finite element modeling, the effect of key parameters on the seismic behavior of a multi-story building resting on a piled raft foundation system is studied to investigate the interaction between the soil, the piled raft foundation, and the superstructure. This research aims to study the seismic behavior of connected piled rafts and to study the behavior of the reinforced concrete structure above in terms of settlement, horizontal displacement values, pile safety, and the resulting internal forces in piles due to earthquake excitation. Study results show that while decreasing the number of piles can achieve allowable settlement limits (the primary purpose of combined piled raft foundation systems in soft clay formations), the piles become more susceptible to bending or shear failures, especially during seismic excitation. Accordingly, the use of piled raft foundation should be used with caution in earthquake-prone areas. It is strongly recommended to increase the piles used beyond what is specified in the static design, according to the expected acceleration level.</p>