ABSTRACT The SpyTag/SpyCatcher system is a modular protein assembly tool based on isopeptide bond‐mediated covalent conjugation, distinguished by mild reaction conditions, rapid ligation rate, and independence from exogenous enzymes or chemical reagents. Owing to its high efficiency, orthogonality, and stability, it has exhibited multi‐dimensional application value in the food sector, enabling the enhancement of enzyme stability and reusability in food enzyme engineering, efficient product synthesis and metabolic optimization in microbial fermentation, high‐sensitivity recognition of mycotoxins in detection, as well as toxin degradation and antimicrobial film construction in preservation packaging. Despite challenges such as large‐scale production and safety evaluation, future advancements through molecular design optimization and interdisciplinary technology integration are expected to accelerate the development of the food industry, providing revolutionary solutions for green processing and food safety.