The aim of this work was to study the effect of a recombinant superoxide dismutase (rSOD) from Bacillus pumilus E−1-1-1 regarding the degradation of aflatoxin M1 (AFM1) in model solution. The degradation mechanism was further explored and applied in milk and beer. The Kinetic Momentum and maximal velocity of the rSOD towards AFM1 were 3.6 μg/mL and 1.8 μg/mL/min, respectively. The rSOD-mediated AFM1 degradation product was identified as C12H11O3. Molecular docking simulation suggested that hydrogen bonds, van der Waals interaction, and pi bond played major roles in the steadiness of AFM1-rSOD. Meanwhile, compared with identical concentration of AFM1, the survival rate of Hep-G2 cells treated with superoxide dismutase-generated AFM1 degradation products increased about 1.6 times. In addition, the degradation rates in lager beer and milk were 15.19% and 26.03%, respectively. Therefore, the rSOD has great modification value to accommodate AFM1 degradation in beer and milk. This study indicates a direction to be followed for future degrading AFM1 in food.