As naturally occurring compounds widely present in plants, food-derived flavonoids have shown great potential in the functional food industry due to their beneficial physiological activities. This article provides a comprehensive review of the structural properties, dietary sources, and recent advances in the application of flavonoids in functional food products. The distribution of flavonoids across plant families and genera is outlined to identify their natural sources. It focuses on the structure-activity relationships of structurally diverse flavonoids including flavones, flavonols, flavanones, isoflavones, chalcones, anthocyanins, and flavanols, as well as on the effects of the structural features of food-derived flavonoids on their bioavailability and functional activity during food processing. To improve the utilization efficiency of foodderived flavonoids, this work proposes multifaceted modification and processing strategies based on flavonoid structural characteristics for enhancing their stability, bioavailability, and functionality, thereby providing a theoretical foundation and technical support for the industrial application of flavonoids.