Catalytic hydrogenations constitute economic and clean transformations to produce pharmaceutical and a multitude of fine chemicals in chemical industry. Herein, we report a cationic Ru(II) complex intercalated into zirconium phosphate (ZrP) layers that enables the efficient catalytic conversion of furfural and other biomass-derived carbonyl compounds into the corresponding alcohols through selective hydrogenation of C=O group. The ZrP layers acted not only as a support for the Ru-complex, but also as the new ligands to tune the Ru(II) center via forming RuÀ O bond. The resulting catalysts exhibit excellent catalytic performance and can be easily recycled for six times without significant loss of activity and selectivity. The Ru(II) complex-intercalated catalysts have been characterized by XRD, SEM, HRTEM, HAADF-STEM, XPS, FT-IR, DR-UV/Vis, EXAFS and XANES. Especially, it is observed that the appropriate interlayer spacing between ZrP layers is favorable to stabilize the Ru(II) complex. Notably, on the basis of the further characterization and density functional theory (DFT) calculation, it is identified that the interaction of cationic Ru(II) complex and PÀ OH group within ZrP layers leads to the high catalytic performance in selective hydrogenation, and the newly formed RuÀ OÀ P species plays a crucial role in the heterolytic hydrogen activation and selective hydrogenation of biomass-derived compounds containing a carbonyl group.