Flax lignans are abundant plant secondary metabolites in flaxseed, with secoisolariciresinol diglucoside (SDG) content reaching 0.61–1.33% of seed dry weight—substantially higher than levels reported for sesame seeds (0.01–0.03%), cereals (<0.01%), and most legumes (<0.005%). These levels make them natural bioactive compounds with considerable application potential. This review summarizes the biosynthetic pathways, key enzymes, and regulatory mechanisms of flax lignans; describes their major biological activities, including antioxidant, anti-inflammatory, anticancer, cardiovascular protective, and metabolic regulatory effects and possible mechanisms of action; and analyzes current progress in extraction, purification, analytical detection, and application. Key limitations in industrial application include complex extraction procedures, high production costs, lack of unified quality standards, and insufficient clinical evidence. Advanced strategies such as synthetic biology approaches for heterologous production, molecular breeding for high-lignan varieties, and green extraction technologies are discussed as promising solutions. This review is intended to serve as a conceptual reference for subsequent mechanistic studies, product development, and industrial translation of flax lignans in food, pharmaceutical, and cosmetic applications.