Simultaneous hydrogenation of polycyclic aromatic hydrocarbons and sulfur contaminates (dibenzothiophene, DBT) in coal tar remains a challenge for energy utilization and environmental remediation. Herein, Ni3Zn/ZnO–Al2O3 catalysts with different ZnO loading were prepared for deep hydrogenation of phenanthrene (PHE) and synchronous removal of DBT in a fixed-bed reactor. Compared to Ni/Al2O3, the optimal Ni3Zn/ZnO–Al2O3 exhibited superior catalytic performance of 100.0% PHE conversion and 92.5% perhydrophenanthrene selectivity with 100.0% DBT conversion at 300 °C under 6 MPa for 10 h in a fixed-bed reactor. The kinetic study for PHE hydrogenation and mechanism for DBT hydrodesulfurization on Ni catalysts were discussed. Electron transfer from Zn to Ni over the active sites weakened DBT adsorption rather than PHE adsorption. The strong interactions between Ni3Zn and ZnO–Al2O3 supports facilitated sulfur migration from the alloy to intimate ZnO, preventing the deactivation of Ni active centers by sulfur deposition and poisoning.