Alginate lyases, enzymes that degrade alginate into unsaturated oligosaccharides, have attracted significant attention for their potential applications across various fields, particularly in agriculture. This review focuses on the molecular engineering of alginate lyases to enhance their activity, stability, and specificity as well as the agricultural applications of the resulting enzymatic products, known as alginate oligosaccharides (AOS). We start by summarizing the sources and classification of alginate lyases, followed by recent advances in their engineering through directed evolution, rational design, truncation of noncatalytic domains, and conserved domain reconstruction. We then explore the diverse agricultural applications of AOS, including their ability to promote plant growth, to increase the content of active plant components, to extend fruit shelf life, and to enhance plant resistance to abiotic stresses. Furthermore, the potential value of AOS as feed additives and preservatives in shrimp-based products is also assessed. This review will not only lay a solid theoretical foundation but also serve as a catalyst for the innovative development and practical application of high-value enzymatic preparations and utilization of AOS-related products, providing new solutions for sustainable agriculture and the food industry.