The persistence of organic carbon (OC) in natural environments is widely attributed to OC associations with minerals such as iron (Fe) minerals. Carboxyl, a critical structure of OC, can form strong complexes with Fe minerals, but it is still largely unknown about the effects of carboxyl groups on the transformation of Fe oxides and the stabilization mechanisms of OC on Fe oxides at nanoscales. In this study, four carboxylic acids with varying numbers of carboxyl groups (2, 3, 4, and 27 carboxyls) and molecular weight (ranging from 100 to 2000 Da) were added during the coprecipitation of Fe oxides and OC. This approach was taken to systematically elucidate the nanoscale distribution and sequestration mechanisms of carboxyl-containing OC on Fe oxides over different aging periods. Results suggested that ferrihydrite transformed quickly into lepidocrocite, goethite, and magnetite with the presence of Fe(II). The transformation rate of lepidocrocite to goethite slowed with increasing carboxyl number in OC molecules for the low molecular weight carboxylic acids (100–300 Da), but the high molecular weight carboxylic acid (∼2000 Da) promoted ferrihydrite transformation into goethite. Meanwhile, the particle sizes of produced magnetite decreased with increasing carboxyl number in OC molecules. During the mineral transformation, the release of OC from Fe oxides to aqueous solution decreased with increasing numbers of carboxyl groups. Spherical aberration corrected scanning transmission electron microscopy (Cs-STEM) coupled with electron-energy-loss spectroscopy (EELS) suggested that carboxyl-rich OC promoted the formation of abundant defective or porous structures in goethite, resulting in OC accumulation in the bulk areas of goethite, which provided an effective way to sequester OC. The aggregation of high molecular weight OC containing more carboxyl groups with magnetite nanoparticles also played an important role in the preservation of OC. Furthermore, Fourier-transform infrared spectroscopy (FTIR) and near edge X-ray absorption fine structure spectroscopy (NEXAFS) indicated that OC may form bidentate binding with Fe oxides and the binding strength of Fe(III) and OC may change with varying numbers of carboxyl groups. Results in this study provided a comprehensive understanding of the dynamic interactions between OC with different numbers of carboxyl groups and Fe oxides, and shed insights into the nanoscale mechanisms of OC stabilization during Fe oxide transformation process.