Improving the seismic resilience of nuclear power plants (NPP) to withstand super-strong earthquakes is critical for ensuring nuclear safety. Seismic isolation can effectively enhance the structural seismic margins and has significant potential for development in NPPs. Although three-dimensional (3D) base isolation can effectively isolate tri-directional ground motion, it also faces challenges such as the limitations of horizontal and vertical displacements of the isolation layer under super-strong earthquakes. In this paper, a novel hybrid passive control strategy that combines 3D base isolation with geotechnical seismic isolation (GSI) systems is proposed. Furthermore, a nonlinear soil-structure interaction analysis method is developed and the program is validated using numerical examples. Finally, a nonlinear dynamic analysis of a large-scale nuclear island building at a non-bedrock site is conducted to investigate the seismic mitigation effects of a hybrid isolation system under super-strong earthquakes. The research findings demonstrate a significant improvement in the isolation effectiveness of the proposed strategy compared to 3D base isolation, which further reduces the tri-directional seismic responses of NPPs while also exhibits the ability to control the deformation in the isolation layer. The proposed hybrid isolation system can significantly improve the ability of NPPs to withstand super-strong earthquakes and provide support for the hybrid seismic isolation design of NPPs.