In this article, NiW/γ-Al2O3 samples were prepared by consecutive impregnations of a W/γ-Al2O3-based catalyst with aqueous solution of nickel salt. The structural control of the nickel ion precursor in the impregnation solution was achieved by the addition of 1,2-cyclohexanediamine-N,N,N′,N′-tetraacetic acid (CyDTA) as a chelating agent. The influence of pH of this aqueous solution on the NiWS phase formation in the sulfided catalysts was investigated. Coordination structures of the Ni–CyDTA complexes were evaluated by FT-IR and DRS UV–Vis spectroscopies. Sulfided catalysts were characterized by X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (HRTEM) and tested in hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DMDBT) carried out in a batch reactor at 593 K and total H2 pressure of 55 bar. Spectroscopic characterization by DRS UV–Vis showed the predominance of the [Ni(CyDTA)]2− species in solution. Following the impregnation and drying steps, the [Ni(CyDTA)]2− complex showed no apparent changes of its structure, independent of the pH value of impregnation solution. The Ni/W/γ-Al2O3 catalysts ex [Ni(CyDTA)]2− complex exhibited high stability. The presence of CyDTA delayed the reduction of Ni and caused a remarkable decrease of the W-support interaction, thus increasing the formation of NiWS phase upon catalyst sulfiding. The catalyst activity–structure correlation demonstrated that the catalyst activity and selectivity is linked with formation of the most active NiWS phase having single or double WS2 slab structures. The catalyst prepared with [Ni(CyDTA)]2− complex at pH of 4.0 exhibited the largest initial HDS activity, which was approximately triple compared with the CyDTA-free counterpart. For all catalysts, the HDS reaction proceeded via hydrogenation (HYD) and direct desulfurization (DDS) reaction routes, the former being the main reaction route. The addition of chelating agent led to an increase of the selectivity toward HYD route products.