Hydrodeoxygenation (HDO) is an important chemical process to convert lignin to high-energy-density cycloalkanes by removing oxygen-containing functional groups. Herein, a bifunctional metal/acid catalyst of Ru/SHZSM-5-100 (Ru/SHZ5-100) with a large specific surface area, a large average pore diameter, and more external pores was successfully prepared by combining the hydrothermal and simple incipient wetness impregnation methods. The resulting Ru/SHZ5-100 catalyst exhibited the best HDO performance for lignin-derived diphenyl ether (DPE) under extremely mild conditions (150 °C, 1 MPa H2, 2 h). The results revealed that DPE was hydrogenated to oxydicyclohexane first and then quickly converted to the target product cyclohexane. Furthermore, other lignin model compounds could also be converted successfully to corresponding cycloalkanes over Ru/SHZ5-100 in this reaction system. Finally, the relationship between the structure and high performance of Ru/SHZ5-100 was studied. The construction of the Ru/SHZ5-100 catalytic system highlighted a promising way to convert lignin model compounds to oxygen-free fuels and chemicals.