Ginkgo biloba L. is a protected relict species of the genus Ginkgo in the Ginkgoaceae family that is valued for its ornamental, economic, and medicinal properties. Flavonoids, the primary medicinal components in G. biloba, have anti-inflammatory, anticancer, and antioxidant effects. They specifically inhibit xanthine oxidase and platelet-activating factor receptors, making them effective in treating Alzheimer's disease and hypertension. The breeding of G. biloba typically focuses on selecting and cultivating tree varieties with high flavonoid content. At the molecular level, structural genes and regulatory factors (transcription factors and noncoding RNA) can directly control flavonoid biosynthesis, whereas external environmental factors indirectly regulate it. From a production perspective, improving extraction techniques can effectively address current low flavonoid yields. Advanced extraction technologies, which reduce solvent use and increase both efficiency and yield to meet market demand, are emerging. This review highlights structural genes and regulatory factors (noncoding RNAs and transcription factors) involved in flavonoid biosynthesis, explores how abiotic factors influence flavonoid accumulation, and outlines optimal extraction methods for increasing the flavonoid content in G. biloba. Ultimately, this research aims to provide valuable insights for future production practices and scientific research that will enhance the medicinal and commercial value of G. biloba.