Supported WMoNi diesel ultra-deep hydrodesulfurization (HDS) catalysts with enhanced synergetic effects among metal species were prepared with W- and Mo-based hybrid inorganic–organic nanocrystals (HNCs) as the W/Mo precursors. The W- and Mo-based HNCs are monodispersed particles with similar structure. The thus-obtained supported WMoNi catalyst has superior hydrogenation and direct desulfurization activities for dibenzothiophene HDS and dramatically higher fluid catalytic cracking diesel HDS performance than WMoNi/Al2O3 prepared by the impregnation method. This benefits from the bimetallic catalyst precursor WMo/Al2O3, which has highly dispersed W and Mo species and high sulfidability and thus generates a large number of metal sulfide slabs after sulfidation. The highly dispersed W/Mo sulfide slabs provide abundant edge sites for dispersing Ni species, facilitating both textural and chemical synergisms among the sulfide phases and yielding more synergetic NiWMoS active phases. The approach opens a novel route to optimizing the synergetic effects among metal species in supported WMoNi catalysts for diesel ultra-deep HDS.