Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins, posing severe threats to food safety and public health. However, the limited availability of efficient AFB1-degrading strains hinders the discovery of diverse degradation enzymes and restricts their application. This study isolated a highly efficient AFB1-degrading strain, Pseudomonas aeruginosa HNGD-JZ06, from citrus. Whole-genome identification revealed two novel genes: a novel multicopper oxidase (MCO) and a superoxide dismutase (SOD). Following heterologous expression and purification, MCO and SOD achieved 98.6 and 96.0% degradation of AFB1 within 24 h (40 °C, pH 7.0). UPLC-MS/MS confirmed conversion of AFB1 into low-toxicity AFQ1/epi-AFQ1, while zebrafish assays verified reduced toxicity. In corn flour, MCO and SOD achieved 72.7 and 58.5% degradation, underscoring their potential in food and feed detoxification. Collectively, this study isolated a novel bacterial resource and identified unique enzymes with AFB1-degrading activity, offering insights into degradation mechanisms and strategies for mycotoxin control in food systems.