Amorphous ferrihydrite (Fh) is abundant in aquatic environments and sediments, and often coprecipitates with dissolved organic matter (DOM) to form mineral-organic aggregates. The Fe(II)-catalyzed transformation of Fh to crystalline Fe (oxyhydr)oxides (e.g., goethite) can result in the changes of uranium (U) species, but the effects of DOM molecules on the sequestration and stability of U during Fe (oxyhydr)oxides transformation are poorly understood. In this study, the associations of DOM molecules with U during the coprecipitation of DOM with Fh were evaluated, and the effects of DOM molecules on the kinetics of U release during Fe (oxyhydr)oxides transformation were investigated using a combination of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), X-ray photoelectron spectroscopy (XPS), and kinetic experiments. FT-ICR-MS results indicated that, in addition to phenolic and polyphenolic compounds with higher O/C ratios, portions of phenolic compounds with lower O/C ratios and aliphatic compounds were also contributed to UO binding when Fh coprecipitated with DOM. In comparison, phenolic and polyphenolic compounds with higher O/C ratios and condensed aromatics were preferentially retained on Fe (oxyhydr)oxides during the transformation. XPS results further suggested that the coprecipitated DOM molecules facilitated the reduction of U(VI) to U(IV) during the transformation, possibly through providing electrons or acting as electron shuttles. The kinetic experiment results indicated that the transformation processes accelerated U release from Fe (oxyhydr)oxides, but the coprecipitated DOM molecules slowed down U release. Our results contribute to understanding the behaviors of U and predicting the sequestration of U in the environment.