The effects of the method of modifying USY zeolite with nickel on the hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DMDBT) have been investigated. USY zeolites were modified with a small amount of Ni by three different methods, namely, the in situ synthesis method, the ion-exchange method, and the impregnation method, and the resulting Ni-modified USY zeolites were used as supports for NiMo sulfide catalysts. We found that the Ni modification method affects the textural properties, the acidity of the Ni-modified USY zeolites, the Ni-Mo-S active-phase morphology, the dispersion of the active metals, the structure of the Ni-Mo-S active phase, the sulfidation degree of the active metals, the 4,6-DMDBT HDS reaction rate constant, the turnover frequency, and the selectivity of the 4,6-DMDBT HDS pathways. Although the impregnation modification method was found to promote the dispersion of active metals most strongly and the ion-exchange modification method was found to enhance the sulfidation degrees of both Ni and Mo the most strongly, these changes did not enhance the catalyst activity the most significantly. Rather, the best catalytic activity was observed over the NiMo/USNiY catalyst (prepared by the in situ synthesis method), which was closely related to the proportion of NiMoS structures in the Ni-Mo-S active phase. Among the three investigated modification methods, the in situ synthesis method was found to be the most suitable for the purpose of preparing highly active HDS catalysts for 4,6-DMDBT.