This paper presents the effect on the inelastic behavior and structural performance of concrete and filled steel pipe through a numerical method for reliable judgment under various load conditions of the CJS composite structural system. Variable values optimized for the CJS synthetic structural system and the effects of multiple variables used for finite element analysis to present analytical modeling were compared and analyzed with experimental results. The Winfrith concrete model was used as a concrete material model that describes the confinement effect well, and the concrete structure was modeled with solid elements. Through geometric analysis of shell and solid elements, rectangular steel pipe columns and steel elements were modeled as shell elements. In addition, the slip behavior of the joint between the concrete column and the rectangular steel pipe was described using the Surface-to-Surface function. After finite element analysis modeling, simulation was performed for cyclic loading after assuming that the lower part of the foundation was a pin in the same way as in the experiment. The analysis model was verified by comparing the calculated analysis results with the experimental results, focusing on initial stiffness, maximum strength, and energy dissipation capability.