In this study, a novel, simple, high yield, and scalable method is proposed to synthesize highly porous MoS2/graphene oxide (M−GO) nanocomposites by reacting the GO and co-exfoliation of bulky MoS2 in the presence of polyvinyl pyrrolidone (PVP) under different condition of ultrasonication. Also, the effect of ultrasonic output power on the particle size distribution of metal cluster on the surface of nanocatalysts is studied. It is found that the use of the ultrasonication method can reduce the particle size and increase the specific surface area of M−GO nanocomposite catalysts which leads to HDS activity is increased. These nanocomposite catalysts are characterized by XRD, Raman spectroscopy, SEM, STEM, HR-TEM, AFM, XPS, ICP, BET surface, TPR and TPD techniques. The effects of physicochemical properties of the M−GO nanocomposites on the hydrodesulfurization (HDS) reactions of vacuum gas oil (VGO) has been also studied. Catalytic activities of MoS2-GO nanocomposite are investigated by different operating conditions. M9-GO nanocatalyst with high surface area (324 m2/g) and large pore size (110.3 Å), have the best catalytic performance (99.95%) compared with Co-Mo/γAl2O3 (97.91%). Density functional theory (DFT) calculations were also used to elucidate the HDS mechanism over the M−GO catalyst. It is found that the GO substrate can stabilize MoS2 layers through weak van der Waals interactions between carbon atoms of the GO and S atoms of MoS2. At both Mo- and S-edges, the direct desulfurization (DDS) is found as the main reaction pathway for the hydrodesulfurization of DBT molecules.