The process of deep hydrodesulfurization (HDS) in gasoline typically results in the saturation of olefins, leading to significant reductions in octane number. In this work, Y-supported Co(Ni)–Mo catalysts that with different Ni–Co content were prepared by the incipient wetness impregnation method, the structure and properties were characterized and analyzed using HRTEM, XPS, H2-TPR, and NH3-TPD. The isomerization of 1-hexene and 1-octene as well as the HDS of thiophene were studied by using model FCC naphtha. The incorporation of Ni was found to enhance the number of MoS2 stacking layers, thereby improving the degree of sulfurization in Mo and subsequently increasing the desulfurization rate, with a maximum achieved desulfurization rate of 94.7%. When employing a Ni/Co ratio of 3:2, optimal synergy between Ni and Co is achieved, resulting in a greater presence of multi-layer stacked II-Co(Ni)MoS active phases. Additionally, appropriate Brønsted acidity levels are maintained to facilitate efficient olefin isomerization while preserving high HDS activity. As a result, the current isomerization yield stands at 58.2%(mass). These understandings shed light on the development of highly HDS and olefin isomerization catalysts.