Crystalline phase engineering is a prominent strategy for synergistically optimizing the surface–body phases of a catalyst. In this work, TiO2 nanosheets assembled into nanotubes (TNSTs) with two phases, anatase and rutile, were firstly synthesized via crystal engineering by simple thermal annealing. These were subsequently loaded with Ru nanoparticles, with a mean size of 5.0 nm, to create the efficient benzene hydrogenation catalyst Ru/TNSTs. The well-designed nanosheet-tube structure boasts a large specific surface area and excellent transmission channels, which effectively prevents the agglomeration and deactivation of loaded Ru nanoparticles, as well as promoting the internal diffusion in the reaction process of benzene hydrogenation to cyclohexene. Furthermore, titanium dioxide nanosheet-tubes contain numerous Ti3+ defects, which not only improves the overall conversion rate of cyclohexene but also enhances the suppression of cyclohexene adsorption. Most importantly, the titanium dioxide with its two-phase composition of 75 wt% anatase and 25 wt% rutile increases the ratio of electron deficiencies of Ru and promotes cyclohexene desorption. These synergistic properties enhance the selectivity and efficiency of the Ru/TNSTs catalysts, resulting in excellent performance in the hydrogenation of benzene to cyclohexene. In particular, the Ru/TNSTs-4 catalyst (annealed for 4 h), under the specific conditions of 140 °C temperature and 5 MPa hydrogen pressure for the hydrogenation process, achieves a 95% initial selectivity and 51% yield of cyclohexene in the reaction, outperforming most supported Ru-based catalysts. This work may provide new perspectives for designing efficient benzene hydrogenation catalysts via crystalline phase engineering.