This study investigates the effects of the Fluid-Structure-Soil Interaction (FSSI) on the seismic responses of a deeply embedded nuclear facility with large water pools under severe earthquakes. This paper presents new seismic analysis method considering FSSI using 3D FEM for deeply embedded typical RC (Reinforced Concrete) shear wall nuclear buildings. In the new method, the commercial SSI analysis software, ACS SASSI was used with Option AA-F, which treats ANSYS fluid element FLUID80 dynamic matrices in ACS SASSI environment. By using the method it was confirmed that large pool water in the building provides significant local deformation of the pool walls, while the effects on other part of the structures are almost negligible from engineering point of view. To investigate more with the structure behavior during severe earthquakes, the nonlinear behavior of the structure was also taken into account with the new FSSI method using ACS SASSI NQA Option NON. To model the RC wall nonlinear behavior, their nonlinear backbone curves (BBCs) were computed using both Japanese and America standards. Then, the nonlinear analysis responses with both standards were compared. It was confirmed that the nonlinear structure behavior produced a visible shift of the ISRS spectral peak responses to the lower frequencies in comparison with the response of linear analysis. Also, although some significant differences of seismic responses were not observed between Japanese standard and American standard, it was confirmed that the differences of formulae in each code were reflected on their seismic responses.