Abstract: To address the limitations associated with conventional Fenton processes, which often exhibit a restricted pH range and present challenges in terms of catalyst recovery and second pollutant, magnetic heterogeneous halloysite (HNT)/MnFe₂O₄ catalysts were optimally synthesized, which could achieve 90% removal efficiency for 50 mg/L methylene blue (MB) at pH 4–10 and have high hydrogen peroxide (H₂O₂) utilization efficiencies. In addition, the catalysts could be easily separated from a solution through magnetic separation. The degradation efficiency of methylene blue (MB) exhibited remarkable resilience against common aqueous interferents with anions ( \mathrmN\mathrmO_3^- , Cl⁻, \mathrmS\mathrmO_4^2- ) and humic acid, demonstrating negligible inhibitory effects. Notably, carbonate species ( \mathrmC\mathrmO_3^2- and \mathrmH\mathrmC\mathrmO_3^- ) even elicited a promotional effect on the catalytic process. Furthermore, the removal efficiency of MB only decreased by less than 10% in the fifth cycle compared with that of a fresh catalyst. Furthermore, the HNT/MnFe₂O₄ catalyst effectively degraded various organic pollutants, such as benzohydroxamic acid, xanthate, and eosin Y. The excellent catalytic performance of the catalysts was attributed to the synergistic effects between HNT and MnFe₂O₄. The electron paramagnetic resonance spectra and quenching experiments indicated that the main reactive oxygen species that participated in the degradation process were ·OH and \cdot \mathrmO_2^- . ·OH directly attacked MB molecules, and \cdot \mathrmO_2^- accelerated the reduction of metal ions. Therefore, the catalysts showed considerable potential for organic pollutant degradation. This study provides valuable insights into the synthesis of novel catalysts and their practical applications in organic wastewater purification.