Gold/palladium binary catalysts have been widely used to the selective oxidation of glycerol to produce value-added chemicals. However, the essential effect of the structure of Au/Pd binary catalysts on the catalytic performance has not been elucidated yet. In this work, Au, Pd, AuPd alloy, Au@Pd core-shell, and Au-Pd Janus nanoparticle catalysts prepared by sol-immobilization and photochemical deposition methods were employed to the selective oxidation of glycerol toward dihydroxyacetone (DHA). The results showed that the activation of glycerol and oxygen molecule was significantly promoted with the appropriate interaction between Au and Pd atoms. That was, the turnover frequency of glycerol and DHA generation rate over the alloyed AuPd nanoparticles were remarkably higher than those of Au@Pd core-shell and Au-Pd Janus nanoparticle catalysts. It was due to the synergistic effect of Pd and Au atoms remarkably promoted the electron transfer from Pd to Au, resulting in increasing the activity of the exposed Au sites, and moderately inhibiting the activity of the exposed Pd sites, which benefited to generate DHA rapidly. After optimizing, up to 61% yield of DHA was achieved at 87% glycerol conversion over the alloyed AuPd catalyst.