The electrocatalytic oxidation of 5‐hydroxymethylfurfural (HMF) provides a feasible approach for the efficient utilization of biomass. Defect regulation is an effective strategy in the field of biomass upgrading to enhance the adsorption capacity of reactants and thus increase the activity. However, how to select appropriate strategies to regulate the over‐enrichment of reactants induced by excessive oxygen vacancy is still a huge challenge. In this work, the defect‐filling strategy to design and construct an element‐filled oxygen vacancy site layered double hydroxide (S─Ov─LDH) is adopted, which achieves a significant reduction in the electrolysis potential of biomass platform molecule HMF oxidation reaction and a significant increase in current density. Physical characterizations, electrochemical measurements, and theoretical calculations prove that the formation of metal─S bond in the second shell effectively regulates the electronic structure of the material, thus weakening the over‐strong adsorption of HMF and OH− induced by excessive oxygen vacancy, promoting the formation of high‐valence Co3+ during the reaction, and forming new adsorption sites. This work discusses the catalytic enhancement mechanism of defect filling in detail, fills the gap of defect filling in the field of biomass upgrading, and provides favorable guidance for the further development of defect regulation strategies.