The selective activation of C=O bonds was the key challenge in the field of biomass utilization. Researchers worked on this purpose by developing high-active and high-selective catalysts. In this study, a Pd1/α-MoC single-atom catalyst was synthesized and applied in selective hydrogenation of biomass-derived furfural with 96.7% conversion and 92.4% selectivity under a near-room temperature. With various characterizations, the formation of Pd single-atom sites over the surface of α-MoC was confirmed. Then, the dominant structure of Pd single-atom site and the reaction pathway were proposed with experimental and Density Functional Theory (DFT) studies. Compared with undecorated α-MoC, the introduction of Pd single-atom species significantly altered the reaction mechanism from Meerwein-Ponndorf-Verley (MPV) process. Moreover, the Pd single-atoms loading on α-MoC(111) surface notably reduced the energy barriers of H2 activation and C=O bond hydrogenation, which may lead to the improving catalytic performance of α-MoC based catalyst. Hence, this investigation could provide a new strategy and understanding for the development of high-active and low-cost catalysts.