The Fukushima nuclear incident has heightened global concerns about the safety of nuclear facilities, the imperative to enhance the seismic resilience of nuclear power plants (NPPs) has become a pivotal aspect of nuclear safety. This study introduces an innovative hybrid passive control system that integrates three-dimensional (3D) base isolation technology with periodic isolation walls, aiming to bolster the seismic resilience of NPPs against very rare earthquakes. Furthermore, a complete and viable computational procedure was developed to study the nonlinear soil-structure interaction effects with high-precision wave motion analysis. Finally, the efficacy of the innovative control system to improve the seismic resilience of large-scale nuclear island buildings situated on non-rocky sites was assessed. The findings reveal that the system significantly mitigates the distribution of damage to NPPs during very rare earthquake scenarios. Compared to non-isolated NPP, the adoption of a hybrid passive control system reduces structural damage dissipation energy by 97.73 %. The system augments the effectiveness of 3D base isolation technology in reducing dynamic responses; specifically, the floor response spectra at the top position of the nuclear island building in the X, Y, and Z directions were lowered by 62.33 %, 52.03 %, and 84.12 %, respectively. Moreover, the system considerably reduces the deformation of the 3D isolation bearings. The innovative hybrid passive control system helps to enhance the seismic resilience of NPPs.