The interactions between dissolved organic matter (DOM) molecules and minerals play significant roles in affecting the fate of carbon and contaminants in soil environment. However, the mechanisms controlling the variations of DOM molecules distribution during the transformation of Fe (oxyhydr)oxides, and the effects of these variations on contaminant behaviors are still largely unknown. In this study, the dynamic variations of DOM properties and distributions, and the kinetics of uranium adsorption on and desorption from Fe (oxyhydr)oxides during the transformation were investigated, employing a combination of Orbitrap mass spectrometry (MS), high-resolution transmission electron microscopy (HR-TEM), and kinetic experiments. Orbitrap MS results indicated that aliphatic molecules and phenolic and polyphenolic molecules with lower O/C values were preferentially released to solution. HR-TEM results indicated that the coprecipitated DOM molecules by ferrihydrite were mainly released to solution rather than sorbed on the newly formed lepidocrocite or goethite during the transformation. Furthermore, the stirred-flow experiment results suggested that soil DOM significantly reduced the adsorption of uranium on, and accelerated the release of uranium from Fe (oxyhydr)oxides, which was ascribed to the changed distribution of DOM molecules and the structure and composition of Fe (oxyhydr)oxides. Our results contribute to predicting contaminant behaviors in soils.