With the large-scale construction of nuclear engineering projects, low-intensity plant sites are becoming increasingly scarce, while high-intensity plant sites are emerging as potential targets. In high-intensity areas, the destructive impact of vertical seismic components on buildings cannot be overlooked. Therefore, this article presents an analysis and research on three-dimensional seismic isolation schemes for nuclear engineering plants, aimed at enhancing the applicability of existing standardized designs for nuclear power technology at these sites. Based on the characteristics of nuclear engineering plants, this article proposes an overall horizontal seismic isolation scheme and an overall three-dimensional seismic isolation scheme. In this paper, we utilize SAP2000 finite element software for our calculations. By comparing and analyzing the results of the two isolation schemes, we find that the vertical peak acceleration of the overall three-dimensional seismic isolation scheme is significantly lower than that of the overall horizontal seismic isolation scheme. Additionally, the overall three-dimensional seismic isolation scheme achieves the following objectives: (1) the peak acceleration of the three-dimensional seismic isolation structure is reduced by more than 50% in the horizontal direction and by more than 30% in the vertical direction; (2) the horizontal displacement of the isolation layer of the three-dimensional seismic isolation structure under a peak ground acceleration (PGA) of 0.5 g remains within 300 mm.