ZrO2 heterophase structure nanocrystals (HSNCs) were synthesized with tunable ratios of monoclinic ZrO2 (m-ZrO2) to tetragonal ZrO2 (t-ZrO2). The phase mole ratio of m-ZrO2 versus t-ZrO2 in ZrO2 HSNCs was tuned from 40% to 100%. The concentration of the surface hydroxyl groups on m-ZrO2 is higher than that on t-ZrO2. ZrO2 HSNCs have different surface hydroxyl groups on two crystalline phases. This creates more intimate synergistic effects than their single-phase counterparts. The ZrO2 HSNCs were used as effective supports to fabricate heterophase-structured Ru/ZrO2 catalysts for benzene-selective hydrogenation. The excellent catalytic performance including high activity and selectivity is attributed to the heterogeneous strong/weak hydrophilic interface and water layer formed at the m-ZrO2/t-ZrO2 catalyst junction.