A yolk-shell structured Co3S4@CoMoS catalyst was prepared through Oswald ripening method and subsequently used for hydrodesulfurization (HDS) reaction. The shells, constructed from Co-promoted MoS2 nanosheets, possess abundant active sites and facilitate the adsorption of reactants through the development of pore channels. The MoS2 sheets are arranged in a staggered and convoluted manner, creating numerous defect sites. The shorter MoS2 slabs provide a wide distribution of reactive sites, ensuring efficient reactions. The Co3S4 species within the inner core acts as an auxiliary active phase, inducing the hydrogen spillover effect in the HDS system. This facilitates the transfer of active hydrogen species to the CoMoS shell, where both CoMoS and Co3S4 phases synergistically enhance the HDS reaction. The Co3S4@CoMoS catalyst achieved up to 99.2% dibenzothiophene (DBT) conversion and 94.9% 4,6-dimethyldibenzothiophene conversion at the lower dosage (30 mg). The structure-activity relationships between active phase and HDS activity were investigated via in-situ infrared spectroscopy and other characterizations as well as density functional theory calculations.