Flavonoids are important medicinal active ingredients in Ginkgo biloba. However, the contribution of protein post-translational modification (PTM) in flavonoid biosynthesis has not been studied. Acetylation of lysine residues is a reversible protein PTM, which plays a key regulatory role in metabolism. To fully understand the molecular mechanism of flavonoid biosynthesis, the transcriptome, metabolome, proteome and lysine acetylome of different tissues of G. biloba were comprehensively analyzed.