A series of NiMo catalysts supported on 3-Dimension cubic Ia 3¯d mesoporous KIT-6 silica were prepared by co-impregnation method using citric acid (CA) as chelating agent to adjust the sulfidation and dispersion degrees of active phase. Dried catalysts without calcination were tested in the hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DMDBT). Impregnation solutions, supports, and catalysts were characterized by means of UV–Vis, Raman, TEM, XRD, N2-physisorption, H2-TPR, elemental analysis, XPS, and HRTEM. The addition of CA results in the formation of MoO3(H2cit)− and Ni(Hcit)(cit)3− complexes, which favors the formation of well dispersed active NiMoS phase. Sulfidation and dispersion degrees of the active phase (average slab length and stacking number of MoS2 particles) could be modulated by adding different amounts of CA. The addition of CA exhibited a promotion effect on hydrogenation (HYD) route and activities and selectivities to HYD of different catalysts were related to the CA contents. NiMoKC2 catalyst with the molar ratio of CA/Ni = 2 exhibited the highest reaction rate of 3.1 × 10−4 mol g−1 h−1 and the highest HYD selectivity of 86% in the HDS of 4,6-DMDBT.