Flavonoids have many beneficial health effects, such as antimicrobial, antioxidant, antiviral, antiplatelet, anti-ischemic, antitumor, anti-inflammatory, antiallergic, estrogenic, and radical-scavenging activity. However, their practical applications are often strongly limited due to low solubility and stability in hydrophilic media. Biocatalysis and biotransformation of flavonoids have been introduced to modify their structure and increase natural flavonoid diversity, which could alter physicochemical properties and improve the bioavailability and biological properties of maternal compounds. In this paper, biocatalytic structural modification of flavonoids by different kinds of enzymes or microorganism, the process and possible mechanism were discussed. The main achievements and key factors affecting biocatalysis of flavonoids were discussed and the research prospect was outlined. Biocatalysis refers to the use of living (biological) systems or their parts to speed up (catalyze) chemical reactions. In biocatalytic processes, natural catalysts, such as enzymes, perform chemical transformations on organic compounds. Both enzymes that have been more or less isolated and enzymes still residing inside living cells are employed for this task