Abstract: A H2O2 etching strategy was adopted to introduce coordinatively unsaturated sites (CUS) on MoS2-based catalysts for dibenzothiophene (DBT) hydrodesulfurization (HDS). The CUS concentrations on MoS2 slabs were finely regulated by changing the concentrations of H2O2 solution. With the increasing H2O2 concentrations (0.1–0.3 mol/L), The CUS concentrations on MoS2 slabs increased gradually. However, the high-concentration H2O2 etching (0.5 mol/L) increased the MoOxSy and MoO3 contents on MoS2 slabs compared to etching with the H2O2 concentration of 0.3 mol/L, which led to the less CUS concentration in the sulfided Mo–H-0.5 catalyst than in the sulfided Mo–H-0.3 catalyst. A microstructure-activity correlation indicated that the CUS introduced by H2O2 etching on MoS2 slabs significantly enhanced DBT HDS. Different Co loadings were further introduced into Mo–H-0.3, which had the most CUS concentration, and the corresponding 0.2-CoMo catalyst with the highest CoMoS content (3.853 wt%) exhibited the highest reaction rate constant of 6.95 × 10−6 mol g−1 s−1 among these CoMo catalysts.