Malonic acid possessing two carboxylic acid anchoring groups is employed as the anchoring group to attach molecular dyes onto IrO2 nanoparticles to oxidize water in a dye-sensitized water splitting system. Yet, the detailed binding modes and nanoscopic structures of malonic acid on the IrO2 substrate are not thoroughly investigated due to the sophisticated structure. Previous researches assume that malonic acid interacts with the IrO2 nanoparticles via two carbonyl groups. In this study, we present first principles calculations on the interfacial structures of malonic acid/IrO2 and state that this assumption is incorrect. Instead, we propose that multiple stable adsorption modes are available at the molecule/IrO2 interface. The associated electronic properties corresponding to different binding modes are discussed.