Catalytic oxidation at mild conditions is crucial for mitigating the high pressure and high temperature challenges associated with current catalytic wet air oxidation (CWAO) technologies in wastewater treatment. Among potential materials for catalytic oxidation reactions, polycrystalline MnO2 existed in natural minerals holds considerable promise. However, the relationships between different crystal phases of MnO2 and their catalytic activity sources in aqueous phase remain uncertain and subject to debate. In this research, we synthesized various MnO2 crystal phases, comprising α-, β-, δ-, γ-, ε-, and λ-MnO2, and assessed their catalytic oxidation efficiency during low-temperature heating for treatment of organic pollutants. Our findings demonstrate that λ-MnO2 exhibits the highest catalytic activity, followed by δ-MnO2, γ-MnO2, α-MnO2, ε-MnO2, and β-MnO2. The variations in catalytic activity among different MnO2 are attributed to variances in their oxygen vacancy abundance and redox activity. Furthermore, we identified the primary active species, which include Mn3+ and superoxide radicals (•O2–) generated by surface lattice oxygen of MnO2. This research highlights the critical role of crystal phases in influencing oxygen vacancy content, redox activity, and overall catalytic performance, providing valuable insights for the rational design of MnO2 catalysts tailored for effective organic pollutant degradation in CWAO applications.