Au nanoclusters with an average size of approximately 1 nm size supported on HY zeolite exhibit a superior catalytic performance for the selective oxidation of 5‐hydroxymethyl‐2‐furfural (HMF) into 2,5‐furandicarboxylic acid (FDCA). It achieved >99 % yield of 2,5‐furandicarboxylic acid in water under mild conditions (60 °C, 0.3 MPa oxygen), which is much higher than that of Au supported on metal oxides/hydroxide (TiO2, CeO2, and Mg(OH)2) and channel‐type zeolites (ZSM‐5 and H‐MOR). Detailed characterizations, such as X‐ray diffraction, transmission electron microscopy, N2‐physisorption, and H2‐temperature‐programmed reduction (TPR), revealed that the Au nanoclusters are well encapsulated in the HY zeolite supercage, which is considered to restrict and avoid further growing of the Au nanoclusters into large particles. The acidic hydroxyl groups of the supercage were proven to be responsible for the formation and stabilization of the gold nanoclusters. Moreover, the interaction between the hydroxyl groups in the supercage and the Au nanoclusters leads to electronic modification of the Au nanoparticles, which is supposed to contribute to the high efficiency in the catalytic oxidation of HMF to FDCA.