Hydrodesulfurization (HDS) is an important process for the production of clean fuel oil, and the development of a new environmentally friendly, low-cost sulfided catalyst is key research in hydrogenation technology. Herein, commercial bulk MoS 2 and NiCO 3 •2NiOH 2 •4H 2 O were first hydrothermally treated and then calcined in a H 2 or N 2 atmosphere to obtain Ni−MoS 2 HDS catalysts with different structures. Mechanisms of hydrothermal treatment and calcination on Ni−MoS 2 catalyst structures were investigated by X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), electron paramagnetic resonance (EPR), and X-ray photoelectron spectroscopy (XPS). The catalytic performance of Ni−MoS 2 catalysts was evaluated by the HDS reaction of dibenzothiophene (DBT) on a fixed bed reactor, and the structure−activity relationship between the structures of the Ni−MoS 2 catalyst and the HDS of DBT was discussed. The results showed that the lateral size, the number of stacked layers, and the S/Mo atomic ratio of MoS 2 in the catalyst decreased and then increased with the increase of the hydrothermal treatment temperature, reaching the minimum at the hydrothermal treatment temperature of 150 °C, i.e., the lateral size of MoS 2 in the catalyst was 20−36 nm, the number of stacked layers of MoS 2 was 5.4, and the S/Mo ratio in the catalyst was 1.80. In addition, the effects of different calcination temperatures and calcination atmospheres on the catalyst structures were investigated at the optimum hydrothermal treatment temperature. The Ni− Mo−S and Ni x S y ratios of the catalysts increased and then decreased with the increasing calcination temperature under a H 2 atmosphere, reaching a maximum at a calcination temperature of 400 °C. Therefore, DBT exhibited the best HDS activity over the H-NiMo-150−400 catalyst, and the desulfurization rate of DBT reached 94.7% at a reaction temperature of 320 °C.