Display omitted •Pd1 SAC exhibits expressively high butenes selectivity.•Hydrogenation reactions follows the pseudo Horiuti-Polanyi mechanism.•1,3-butadiene adsorbs on Pd1 in a mono-π mode, distinct from that on Pd bulk.•The proximity O atom is found to be crucial for facilitating H2 dissociation. Supported metal single-atom catalysts (SACs) with maximized metal atom efficiency and unique catalytic properties have drawn tremendous attention in the catalysis field. In this work, we reported that in selective hydrogenation of 1,3-butadiene, graphene supported Pd1 single atoms, synthesized by atomic layer deposition, exhibited expressively 100% butenes selectivity at 100% conversion at near ambient temperature, regardless of hydrogen partial pressures. The hydrogen reaction order was found to be about 1.2, indicating that hydrogenation dissociation is the rate-determining step. Combining with other structural characterization techniques, in situ X-ray absorption fine structure spectroscopy suggests that the Pd1 single atom likely bonds to the graphene support through three PdC and one PdOC coordinations. Density functional theory calculations show that 1,3-butadiene adsorbs on Pd1 via a mono-π adsorption mode (−0.98 eV), much stronger than that of H2 (−0.30 eV), which makes Pd1 to be predominantly covered with a 1,3-butadiene molecule during reaction, consistent very well with the results of H-D exchange reaction. Facilitated by the bridging O atom in the PdOC coordination, H2 dissociates at the 1,3-butadiene covered Pd1 atom in the heterolytic way, then hydrogenates the adsorbed 1,3-butadiene molecule by following the pseudo Horiuti-Polanyi mechanism. Distinct from its adsorption on extended Pd surfaces, such mono-π adsorption of 1,3-butadiene on Pd1 favors 1-butene formation, but impedes the secondary hydrogenation to butane owing to intensified steric hindrance, thus yielding the expressively high butenes selectivity over Pd1 SAC. These findings pave a new way to rational design SACs catalyst in selective hydrogenation reactions.