Herein, HSnY zeolites were synthesized through in-situ modification and employed as NiW catalyst supports for ultra-deep hydrodesulfurization (HDS) of model diesel. The effects of Sn incorporation on the material and catalyst properties were systematically characterized. The results reveal that in-situ incorporated Sn modifies the interatomic distances in the FAU framework, leading to lattice strain and forming new Si-O-Sn bonds, which affects the coordination environment of Si and Al. Simultaneously, incorporating Sn into the framework significantly enhances the acid density and shifts the d-band center of NiWS due to the stronger electronic properties of Si-O-Sn bonds. This alteration facilitates electron transfer, weakens active metals-support interactions, and promotes the formation of highly active NiWS phase during sulfidation. Therein, point-to-point adsorption of 4,6-DMDBT at the NiWS corner sites is significantly enhanced. Ultimately, the optimized NiW/HSnY-3 catalyst achieves a remarkable 99.2% conversion of 4,6-DMDBT (280 °C) due to optimized Wsulfidation, high NiWS phase concentrations, and abundant acid sites. This work elucidates Sn-doping’s role in tailoring NiWS phase structure for ultra-deep HDS, offering a design strategy for efficient diesel HDS catalysts.