N,N-Dimethyldodecylamine N-oxide (DDAO), PVP and PVA capped supported AuPd bimetallic nanoparticles (NPs) were prepared, and their catalytic activities were evaluated for the oxidation of 1,6-hexanediol (HDO) to 6-hydroxycaproic acid (HCA) using H2O2 in basic aqueous solution. Among three catalysts, DDAO capped AuPd bimetallic NPs catalysts exhibited superior selectivity for HCA formation than PVP and PVA capped catalysts. To explain the difference in the catalytic behavior, the catalysts were characterized thoroughly. XRD, TEM and STEM-HAADF-EDS studies were employed to identify the structure and morphology of capped AuPd-NPs, respectively. The chemical and electronic states were elucidated using XPS and XAS methods. The characterization data revealed that the capping agent significantly influences the electron density on metals and extent of alloying between Au and Pd metals. It was revealed that DDAO-capped catalyst induces appropriate negatively charged Au species with a few numbers of Au–Pd interfaces for the highly selective formation of HCA via HDO oxidation in basic aqueous media. Furthermore, other aliphatic diols, 1,7-heptanediol, 1,8-octanediol and 1,2-hexanediol, were also selectively oxidized on AuPd-DDAO catalysts toward the corresponding ω-hydroxycarboxylic acids in high yields.