Abstract: Based on the values of flavonoids research and application in Ginkgo biloba forest cultivation, drug production, we reviewed recent progress of flavonoids metabolic regulation in environment, cell culture and molecular level in this paper. It was concluded that the changes of light, temperature, water and other environmental conditions could regulate the metabolism of G. biloba flavonoids. The induction of elicitors and trace elements was effective method to regulate the production of flavonoids in cell culture. With the complete genome sequencing of G. biloba, many key enzyme genes and transcription factors have been discovered through genomics and high-throughput sequencing technology, and this enriched the control ways of the flavonoids metabolism in G. biloba. In the future, more related genes and key enzymes should be excavated through multi-omics research, and it is necessary to research the metabolic pathway of flavonoids by using upstream and downstream of gene clusters combined regulation, and to intelligently regulate of G. biloba flavone synthesis by combining with synthetic biology.