The increasing intensity of human activities has led to a critical environmental challenge: widespread metal pollution. Manganese (Mn) oxides have emerged as potentially natural scavengers that perform crucial functions in the biogeochemical cycling of metal elements. Prior reviews have focused on the synthesis, characterization, and adsorption kinetics of Mn oxides, along with the transformation pathways of specific layered Mn oxides. This review conducts a meticulous investigation of the molecular-level adsorption and oxidation mechanisms of Mn oxides on hazardous metals, including adsorption patterns, coordination, adsorption sites, and redox processes. We also provide a comprehensive discussion of both internal factors (surface area, crystallinity, octahedral vacancy content in Mn oxides, and reactant concentration) and external factors (pH, presence of doped or pre-adsorbed metal ions) affecting the adsorption/oxidation of metals by Mn oxides. Additionally, we identify existing gaps in understanding these mechanisms and suggest avenues for future research. Our goal is to enhance knowledge of Mn oxides' regulatory roles in metal element translocation and transformation at the microstructure level, offering a framework for developing effective metal adsorbents and pollution control strategies.