Mesoporous zeolite ZSM-S (ZSM-S-M) was synthesized and used as support for the preparation of highly efficient nickel phosphide catalyst (Ni2P/ZSM-S-M) in the deep hydrogenation of phenanthrene and in the hydrodesulfurization (HDS) of 4,6-dimethyldibenzothiophene (4,6-DM-DBT). Compared with Ni2P catalysts supported silica and high surface area hexagonal mesoporous silica (HMS) (Ni2P/SiO2 and Ni2P/HMS), Ni2P/ZSM-S-M exhibits higher hydrogenation and HDS activity. The phenanthrene conversion and deep hydrogenation products selectivity over Ni2P/ZSM-S-M (95% and 83%) are much higher than those over Ni2P/SiO2 (61% and 73%) and Ni2P/HMS (69% and 4S%) under mild conditions. The 4,6-DM-DBT conversion over Ni2P/ZSM-5-M (93%) was higher than that over Ni2P/SiO2 (62%). This feature is attributed to the difference in surface properties of support. A large amount of acidic hydroxyl groups on the zeolites can interact strongly with catalyst precursor, resulting in the formation of highly dispersed Ni2P particles with small sizes, which provide abundant hydrogenation active sites.