Manganese peroxidase (MnP), a vital extracellular enzyme for the degradation of lignin and other organic pollutants, has demonstrated immense potential for agricultural and environmental applications, including straw pretreatment, feed fermentation, mycotoxin degradation, and water treatment. However, current research remains in its exploratory phase, with naturally sourced MnP unable to meet industrial-scale demands and no mature commercial enzyme preparations available on the market. This comprehensive review innovatively constructs a framework for MnP research, probing into its molecular conformation and catalytic principles, while providing an overview of the advancements in high-throughput screening and In silco designing strategies. Specifically, this review focuses on the practical applications of MnP in sustainable agriculture, elaborating on its potential and challenges in straw resource utilization, efficient feed fermentation, mycotoxin control, and water quality improvement. Furthermore, this review summarizes the recent achievements in optimizing MnP activity through enzyme engineering techniques and discuss customized mutation strategies tailored to specific agricultural and environmental requirements, thereby laying a solid theoretical foundation and scientific basis for the industrial production and commercialization of MnP.