The SnSAPO-5 molecular sieve containing divalent tin in the framework was successfully synthesized and analyzed by XRD, XPS, XRF, N 2 -asdorption desorption isotherms, NH 3 -TPD, Py-IR, and 27 Al and 31 P NMR. The results show that the trivalent aluminum is substituted by divalent tin in the framework of SnSAPO-5, generating a P((4−n)Al,nSn) (n = 1− 4) environment, which increases the number of Lewis and Brønsted acid sites. The five catalysts (NiW/SAPA, NiW/SnSAPA, NiW/APA, NiW/SnAPA, and NiW/EPA) with the same content of active metals were obtained by the incipient wetness coimpregnation method. The catalyst NiW/SnSAPA with higher k HDS and TOF exhibited a much higher HDS rate of 4,6dimethyldibenzothiophene (4,6-DMDBT) (85%) at 280 °C, while the HDS rates over the other catalysts are less than 40% (24%, 34%, 37%, and 29%, respectively), which is attributed to the catalyst NiW/SnSAPA possessing more suitable acidic sites, a higher sulfidation degree of W species, and a higher stacking number of WS 2 slabs. Futhermore, the catalyst NiW/SnSAPA has a much higher HDS rate (85%) for 4,6-DMDBT and exhibits a much higher performance of deep hydrodesulfurization in comparison to the catalyst NiW/EPA prepared with an industrial support (29%) at 280 °C. This finding has great practical significance for the development of ultradeep HDS industrial catalysts.