Co‐based spinel oxides, which are of mixing valences with the presence of both Co2+ and Co3+ at different atom locations, are considered as promising catalysts for the electrochemical oxidation of 5‐hydroxymethylfurfural (HMF). Identifying the role of each atom site in the electroxidation of HMF is critical to design the advanced electrocatalysts. In this work, we found that Co2+Td in Co3O4 is capable of chemical adsorption for acidic organic molecules, and Co3+Oh play a decisive role in HMF oxidation. Thereafter, the Cu2+ was introduced in spinel oxides to enhance the exposure degree of Co3+ and to boost acidic adsorption and thus to enhance the electrocatalytic activity for HMF electrooxidation significantly. The exploration of optimal geometrical site in Co3O4 for electrochemical HMF oxidation by the building tetrahedral (Zn2+) and octahedral (Al3+) blocks is described. The electrochemical results demonstrate that Co3+Oh are the best geometrical sites for HMF oxidation, and the chemical adsorption for acidic organic molecules is dominated by Co2+Td. The exposure degree of Co3+ is improved by Cu2+ and thus results in a record activity.