The preparation of high activity bifunctional catalysts, especially hierarchical porous zeolite-supported metal catalysts, are of great important for efficient converting the heteroatom-containing organic species to high quality clean fuels. An excellent performance Ni catalyst was prepared by loading highly dispersed Ni nanoparticles (NNPs, ca. 10%) on Y/Beta composite zeolite (YBCZ) and denoted as Ni10%/YBCZ. Low-temperature coal tar was efficiently extracted with petroleum ether, methanol, and carbon disulfide (CDS) at room temperature under ultrasonic irradiation to obtain CDS extractable portion (EPCDS) in the yield of 20.1%. According to the analysis with a GC/MS, EPCDS consists of chain alkanes (CAs, 4.0%), oxygen-containing organic compounds (OCOCs, 56.0%), arenes (35.3%), nitrogen-containing organic compounds (NCOCs, 3.3%), and sulfur-containing organic compounds (SCOCs, 1.4%). It was subjected to catalytic hydroconversion (CHC) over Ni10%/YBCZ at 160 °C for 18 h under 5 MPa of initial hydrogen pressure to obtain EPCHC. The results show that all organic species in EPCDS were completely converted to CAs (9.0%), cycloalkanes (70.8%), and hydroarenes (20.2%). In Ni10%/YBCZ, hierarchical porous zeolite-zeolite composite with strong Lewis acid sites in its crystal texture and highly dispersed NNPs play crucial roles in removing heteroatoms and hydrogenating aromatic rings, respectively. Oxydibenzene, a model compound with > Car-O bridge bonds and aromatic rings, was used to investigate the catalytic activity of Ni10%/YBCZ. Oxydibenzene was effectively converted to cyclohexane, bicyclohexane, and tercyclohexane over Ni10%/YBCZ in n-pentane at 160 °C for 2 h under 5 MPa of initial hydrogen pressure, indicating that Ni10%/YBCZ has excellent activity in CHC process under mild conditions.