Fragaria moupinensis is a tetraploid strawberry species native to China， offering both edible and medicinal benefits. However， research on the bioactive compounds present in F. moupinesis fruits remains limited. This study combined metabolomic and transcriptomic analyses to identify key bioactive substances in F. moupinensis fruit， investigate their dynamic changes during ripening， and elucidate the underlying molecular mechanisms of their biosynthesis. Metabolomic analysis revealed that pathways related to ABC transporters， phenylpropanoid biosynthesis， galactose metabolism， and flavonoid and flavonol biosynthesis are involved in the regulation of fruit ripening in F. moupinesis. And the levels of multiple bioactive flavonoids， flavonols， flavone， flavanones， and isoflavones—including morin， avicularin， rhoifolin， kaempferol-3-O-galactoside， eriocitrin， and genistein， which possess antioxidant and anti-inflammatory activities—progressively increased during fruit maturation. Transcriptomic analysis revealed that pathways related to flavonoid biosynthesis， glycolysis/gluconeogenesis， and the citrate cycle are involved in the regulation of fruit ripening in F. moupinensis. Integrated transcriptomic and metabolomic analyses revealed that the phenylpropanoid biosynthesis pathway plays a crucial role in the biosynthesis of these key active compounds. This research provides a theoretical foundation for enhancing the medicinal value of F. moupinensis and for the genetic improvement of cultivated strawberry varieties.