Red yeast rice (RYR), a traditional fermented product obtained via rice fermentation with Monascus purpureus, has a millennia-long history of culinary and medicinal use in East Asia and has gained global attention as a prominent functional food ingredient for its well-recognized cholesterol-lowering properties. This review is driven by one core question: How can the dual challenges of standardizing key bioactive constituents, particularly monacolin K (MK), while eliminating the mycotoxin citrinin be addressed through biotechnological and analytical advances? This narrative review consolidates the latest research progress on RYR-derived bioactive compounds, with a specific focus on their production optimization, multifaceted health-promoting potentials, safety regulation, and application prospects in health food development. We elaborate on key advances in fermentation biotechnology and strain engineering for enhancing the yield of the core lipid-lowering component MK while eliminating the nephrotoxic mycotoxin citrinin, and comprehensively summarize the synergistic bioactivities of RYR metabolites beyond MK. The current applications of RYR in functional foods, dietary supplements, and traditional fermented products are detailed, alongside a comparison of the divergent regulatory frameworks for RYR across major global markets. Finally, we identify critical bottlenecks restricting RYR industrialization, including extreme inter-product heterogeneity and global regulatory fragmentation, and propose evidence-based future research directions to facilitate the development of safe, standardized, and effective RYR-based health foods.