Due to multiple degrees of freedom, evaluating high-rise buildings’ seismic safety under unpredictable seismic excitations is difficult. To address the issue that the damage mechanism of a mega-subcontrolled structural system (MSCSS) has not yet been studied, this paper employs ABAQUS software with strong nonlinear analysis capabilities to analyze the nonlinear elastic‒plastic time history of an MSCSS, analyze structural damage to the MSCSS structure, reveal the internal energy dissipation mechanism of the MSCSS, and evaluate the damping performance of the MSCSS structure. This work presents a novel and optimized MSCSS structure equipped with SPSW that improves the system’s seismic performance. First, a refined finite element model of the MSCSS is established, and the impact of vigorous seismic excitations on the damage to the MSCSS structure is considered. The MSCSS structure’s vulnerable parts are then summarized using stress nephograms and residual stresses. Finally, the favorable damping performance of the structure reveals that the newly proposed structure has good shock absorption performance based on an analysis of the energy dissipation, time history, and interstory drift of the MSCSS. This paper’s research findings elaborate the structural damage trend in MSCSS structures, which can serve as a theoretical foundation for MSCSS structure damage identification.