Manganese dioxide (MnO2), renowned for its abundant natural crystal phases, emerges as a leading catalyst candidate for the degradation of pollutants. The relationship between its crystal phase and catalytic activity, particularly for periodate activation, has remained both ambiguous and contentious. This study delineates the influence of various synthetic MnO2 phase structures on their capabilities in catalyzing periodate-assisted pollutant oxidation. Five distinct MnO2 phase structures (α-, β-, γ-, δ-, and ε-MnO₂) were prepared and evaluated to activate periodate and degrade pollutants, following the sequence: α-MnO₂ > γ-MnO₂ > β-MnO₂ > ε-MnO₂ > δ-MnO₂. Through quenching experiments, electron paramagnetic resonance tests, and in situ electrochemical studies, we found an electron transfer-mediated process drive pollutant degradation, facilitated by a highly reactive metastable intermediate complex (MnO₂/PI*). Quantitative structure-activity relationship analysis further indicated that degradation efficiency is strongly associated with both the crystal phase and the Mn (IV) content, highlighting it as a key active site. Moreover, the α-MnO₂ phase demonstrated exceptional recycling stability, enabling an effective pollutant removal in a continuous flow packed-bed reactor for 168 h. Thus, α-MnO₂/PI proved highly effective in mineralizing organic pollutants and reducing their toxicities, highlighting its significant potential for environmental remediation.