Flavonoids, a kind of secondary metabolites with both edible, medicinal and antioxidant purposes, could be widely used in food, drug processing, forest products, chemical industry and many other fields. Flavonoid production in plant organs were influenced by numerous internal and external factors at various stages, leading to differential gene expression and transcription factors activity. This study reviews the characteristics of major flavonoids categories, their distribution and accumulation in different plant parts and analyzing their molecular mechanisms. The results showed that: (1) Flavonoids exhibited wide distribution in all parts of the plants, with higher concentrations found in shoots system compared to roots sytem, across most species (predominantly accumulated in leaves and flowers). Plant sex, specific growth and development stages are both impacting indicators; (2) Cultivation methods and abiotic stress could affect plants flavonoid biosynthesis, while inappropriate physical treatments and cultivation methods induced stress in plants, prompting the activation of antioxidant mechanisms for flavonoid synthesis as a defence strategy via indirect pathways; (3) Various key genes and transcription factors collaboratively influenced key enzymes activities and regulate flavonoid biosynthesis, forming a complex regulatory network among these genes and transcription factors; (4) Further studies are required to elucidate whether flavonoid synthesis under various cultivation measures follows direct or indirect pathways. Furthermore, exploring methods for flavonoid biosynthesis and accumulation in specific organs or tissues, as well as identifying plant tissues and microorganisms with high efficiency in flavonoid biosynthesis, is essential for achieving targeted cultivation of plants and quantitative flavonoid production.