A charge mismatch between transition-metal-ion dopants and metal oxide nanoparticles (MO NPs) within an engineered complex engenders a significant number of oxygen vacancies (VO) on the surface of the MO NP construct. To elucidate in-depth the mechanism of this tendency, Co ions with different charge states (Co3+ and Co2+) were doped into ZnO NPs, and their atomic structural changes were correlated with their photocatalytic efficiency. We ascertained that the increase of the Zn-O bond distances was distinctly affected by Co3+-ion doping, and, subsequently, the number of VO was noticeably increased. We further investigated the mechanistic pathways of the photocatalytic oxidation of 2,5-hydroxymethylfurfural (HMF), which have been widely investigated as biomass derivatives because of their potential use as precursors for the synthesis of sustainable alternatives to petrochemical substances. To identify the reaction products in each oxidation step, selective oxidation products obtained from HMF in the presence of pristine ZnO NPs, Co3+- and Co2+-ion-doped ZnO NPs were evaluated. We confirmed that Co3+-ion-doped ZnO NPs can efficiently and selectively oxidize HMF with a good conversion rate (∼40%) by converting HMF to 2,5-furandicarboxylic acid (FDCA). The present study demonstrates the feasibility of improving the production efficiency of FDCA (an alternative energy material) by using enhanced photocatalytic MO NPs with the help of the charge mismatch between MO and metal-ion dopants.