Unsupported NiMo catalyst has high hydrogenation activity due to its high active site distribution. However, low specific surface area and pore distribution greatly limit the efficient utilization of the active components. The Y-zeolite nanoclusters were hydrothermally synthesized and introduced into the unsupported NiMo catalysts from a layered nickel molybdate complex oxide. The XRD, N2 adsorption-desorption, FT-IR, Py-IR, SEM, NH3-TPD, and TEM were used to characterize all catalysts. The dibenzothiophene (DBT) hydrodesulfurization (HDS) reaction was performed in a continuous high pressure microreactor. The results showed that the specific surface area, pore volume, and average pore size of the unsupported NiMo catalysts were greatly increased by the Y-zeolite nanoclusters, and a more dispersed structure was produced. Furthermore, the Lewis acid and total acid content of the unsupported NiMo catalysts were greatly improved by the Y-zeolite nanoclusters. The HDS results showed that the unsupported NiMo catalysts modified by the nanoclusters had the same high desulfurization efficiency as the unmodified catalyst, but had more proportion of direct desulfurization (DDS) products. The results offer an alternative to reducing hydrogen consumption and save cost in the production of ultra clean diesel.