Abstract A novel composite material ZSM-5/KIT-6 (ZK-W) was synthesized by enwrapping nano-sized ZSM-5 zeolite crystals with mesoporous KIT-6 silica. This composite was used as catalyst support for NiMo sulfide in the hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DMDBT). The NiMo/ZK-W catalyst showed the highest HDS activity and its 4,6-DMDBT conversion was about double that of a conventional NiMo/Al2O3 catalyst at 320°C, 4.0MPa, and LHSV of 150h−1 and on the basis of sulfur. The superior catalytic performance of NiMo/ZK-W is related to the synergistic effect of the excellent diffusion through the hierarchical porous structure and the suitable Brønsted acid sites. 3,6-DMDBT and 3,7-DMDBT, two isomers of 4,6-DMDBT, were identified simultaneously for the first time in the HDS products of 4,6-DMDBT over the NiMo/ZK-W catalyst. The NiMo/ZK-W catalyst exhibited a superior isomerization ability, and 4,4′-dimethylbiphenyl was the main product, indicating that the isomerization pathway is the main reaction route. A new reaction network of 4,6-DMDBT HDS over NiMo/ZK-W catalyst was proposed.