Flower bud differentiation marks a critical transition period in plants from vegetative to reproductive growth. During this process, flavonoids, a key class of secondary metabolites in plants, do not directly influence flower bud differentiation. Instead, they play a vital role in the morphogenesis and developmental regulation of flower buds, serving as an indispensable material foundation for the normal formation and development of floral organs. They regulate the internal environmental homeostasis required for mango axillary bud differentiation, creating suitable conditions for the transformation of axillary buds into flower buds. Through pathways such as adjusting hormone balance, mediating signal transduction, and maintaining stable cellular metabolism, they indirectly promote the transformation of mango axillary buds into flower buds with corresponding morphological and physiological characteristics. Building upon the research group’s prior findings, this study demonstrated that removing terminal flowers during mango axillary bud conversion could delay flowering. Flower bud differentiation marks a critical transition period in plants from vegetative to reproductive growth. During this process, flavonoid, a key class of secondary metabolites in plants, do not directly influence flower bud differentiation. Instead, they play a vital role in the morphogenesis and developmental regulation of flower buds, serving as an indispensable material foundation for the normal formation and development of floral organs. They regulate the internal environmental homeostasis required for mango axillary bud differentiation, creating suitable conditions for the transformation of axillary buds into flower buds. Through pathways such as adjusting hormone balance, mediating signal transduction, and maintaining stable cellular metabolism, they indirectly promote the transformation of mango axillary buds into flower buds with corresponding morphological and physiological characteristics. Building upon the research group’s prior findings, this study demonstrated that removing terminal flowers during mango axillary bud conversion could delay flowering. This technique effectively mitigates damage from late spring frosts and other cold weather events, offering a crucial technical approach for securing mango yields. To delve into the underlying regulatory mechanisms, axillary buds from the “Guifei” mango cultivar at the Gan Zhuang Town mango base in Yuanjiang county, Yuxi city, Yunnan province (23.4210°N, 102.57189°E) were used as the research material. Axillary buds were collected after apical inflorescence removal and subjected to integrated transcriptomic and metabolomic analysis. This study examined gene expression and metabolic changes related to flavonoid biosynthesis following terminal inflorescence removal, revealing the association between flavonoid biosynthetic pathways and floral bud differentiation to effectively mitigate spring frost damage in mangoes. Results indicated that post-removal, gene expression changes in flavonoid biosynthesis pathways, including CHS1, CHI, F3'H, F3'5'H1, and F3H, affected the production of naringenin chalcone, naringenin, dihydroquercetin, cyanidin, pelargonidin,(+)-gallocatechin,2ʹ,3,4,4ʹ,6ʹ-pentahydroxychalcone, and pinobanksin. This indicates that the CHS1, CHI, F3H, F3'H, and F3'5'H1 genes accelerate the conversion of mango axillary buds into floral buds by regulating flavonoid biosynthesis, thereby promoting the formation of mango floral organs and providing new insights into the association between flavonoid biosynthesis and floral bud differentiation.