Baicalein (5,6,7-trihydroxyflavone) and wogonin (5,7-dihydroxy-8-methoxyflavone), as typical flavonoids isolated from Scutellaria baicalensis, are well important precursors in drug discovery which produce diverse therapeutically related applications in pharmacological practices. Researches in medicinal chemistry field have synthesized baicalein and wogonin derivatives with multiple medicinal properties including antitumor, central nervous system (CNS), anti-inflammatory, antiviral, antimicrobial and hypoglycemic activities. Simultaneously, SAR (Structure-Activity Relationship) analysis has been gradually possessed, along with a great deal of derivatives have been derived for potential targets. In this article, we comprehensively summarize the biological activities and SAR for baicalein and wogonin derivatives, along with the featuring bioactive molecules reported in patents, wishing to provide an overall retrospect and prospect on baicalein and wogonin analogues.