A series of numerical simulations were carried out on two types of superstructures and six types of piled raft foundations to investigate the effects of seismic soil–pile–structure interaction (SSPSI) on the seismic responses of the superstructures. In this research, the effectiveness of a piled raft application was assessed; the pile optimum numbers, locations, and configurations were estimated; and finally, a comparison was made between the nonlinear structural responses of the obtained two-dimensional (2D) and three-dimensional (3D) models. Parametric studies were conducted to achieve strategies for optimized designs of piled raft foundations subjected to the low-to-high intensities of real earthquake records as the input motions. The numerical results represented a reasonable correlation between the shaking intensity rates (SIRs) and maximum interstory drifts of the structures. It was discovered that the performance levels of the structures on a softened ground were a function of the area replacement ratios, lengths, diameters, and spaces between the piles; ground motion features; and height/width ratios of the structures. These important aspects had to be regarded to achieve a reliable design. The aim of this investigation was to ameliorate the characteristics of a system of long–short combined piled raft foundations based on an understanding of the interaction mechanics.