MnO2 plays an important role in protecting/transforming dissolved organic matter (DOM). However, the diversity of MnO2 solid-phase speciation challenges the analysis of DOM-mineral interactions. Herein, the adsorption, protection, and transformation of DOM by MnO2 polymorphs were investigated. Our findings showed that MnO2 with a large specific surface area adsorbs more DOM; however, the protection of DOM is primarily related to the phase structure of MnO2. Compared to the tunnel-structured α- and β-MnO2, the physical entrapment within the layers provided by δ-MnO2 is more conducive to maintaining the stability of DOM. Additionally, δ- and α-MnO2 can generate a large amount of reactive oxygen species (ROS), such as hydrogen peroxide, hydroxyl radical, and superoxide, facilitating the transformation of DOM into low-molecular-weight (m/z 100-333) lignin or inorganic carbon. By contrast, β-MnO2 exhibited negligible ROS production, instead oxidizing DOM through Mn4+ redox to generate midmolecular-weight (m/z 334-566) lignin, proteins, and lipids, and high-molecular-weight (m/z 567-800) lignin and lipids. Our results demonstrate that the MnO2 crystal structure exerts a dominant regulatory influence on DOM protection, whereas the abundance of Mn4+ and ROS determines the transformation of DOM. These findings provide critical insights into the understanding of DOM fate in the environment.