Balancing the Cu+/Cu0 ratio is a common strategy to improve catalytic activity of Cu-based catalysts but is still constrained by low atomic utilization and the inherent nature of charge distribution. Herein, we reported a strategy of replacing the Cu0 active sites in Cu-based catalysts by constructing bimetallic sites on ceria, which consist of spatially separated trace amounts of palladium metal and plate-shaped Cu+ clusters with one-atom layers. The catalytic activity of the prepared Cu100Pd1/CeO2-FA catalyst (using formic acid) was 4 times that of conventional Cu100Pd1/CeO2-H catalyst in selective hydrogenation of 5-hydroxymethylfurfural to 2,5-bis(hydroxymethyl)furan, even outperforming some existing noble metal catalysts. Multiple characterizations and theoretical calculations demonstrated that the Pd atom is the heterolytic activation site for H2 molecules while plate-shaped Cu+ metal clusters act as effective hydrogenation places. This directional control involving both spatial relationship and electronic structure of the active site provides a new strategy for designing hydrogenated catalysts.