The Fukushima nuclear accident in March 2011 has raised more stringent requirements for the ability of nuclear power plants (NPPs) to withstand extreme disasters such as extreme earthquakes. To address this challenge, this study proposed a new hybrid multi-dimensional passive control system that combines three-dimensional base isolation and geotechnical seismic isolation. In this system, high-damper rubber bearings were employed to isolate horizontal seismic motions, whereas disc springs, accounting for frictional forces, were used to mitigate vertical seismic motions. Additionally, a geotechnical seismic isolation system arranged under the base mat was leveraged to further reduce the seismic response of the superstructure. Taking a large-scale reactor building in complex layered sites as an example, the effectiveness of the hybrid multi-dimensional isolation system was studied using a wave motion method. The research results indicate that when subjected to extreme earthquakes, hybrid multi-dimensional isolation exhibits superior isolation performance compared with three-dimensional base isolation, which can significantly reduce the three-dimensional dynamic response of nuclear structures without increasing the displacement of the isolation bearings. The proposed hybrid multi-dimensional isolation system offers an effective solution to the challenges faced by three-dimensional isolation systems, thereby enhancing the seismic resistance of nuclear structures against extreme earthquakes.