Flavonols, flavones, and isoflavones are flavonoids possessing broad pharmacological activities, such as antiviral, anti-inflammatory, and antioxidant effects. Their biosynthetic pathways have been largely elucidated. This article reviews the regulatory patterns and mechanisms mediated by transcription factors for these three types of flavonoids. Research on flavonol regulation involves a wide range of species, while studies on flavone regulation have primarily focused on species within the Lamiaceae, Rutaceae, and Asteraceae families (e.g., Scutellaria baicalensis, citrus, chrysanthemum). Research on isoflavone regulation is mainly concentrated in the Fabaceae family (e.g., soybean). Both positive and negative regulation exist for all three classes, although reports on negative regulation for flavones and isoflavones are relatively scarce. The regulatory patterns of these three flavonoid classes differ from those of anthocyanins and exhibit common regulatory modes, including: (1) Sole regulation by MYB transcription factors, which represents the predominant mode; (2) Sole regulation by other transcription factors; (3) Complex-mediated regulation (e.g., MYB forming binary/ternary complexes with other transcription factors). Based on the types of target genes acted upon, the regulatory mechanisms can be categorized into: multi-target regulation, specific gene regulation (e.g., regulation of FLS for flavonols and FNS for flavones), and regulation of glycosylation genes. Additionally, these mechanisms include cascade regulation and competitive regulation (the latter is primarily observed in flavonols). This review provides a reference for in-depth analysis of the transcriptional regulatory networks governing the biosynthesis of these three bioactive flavonoid classes, thereby facilitating related research in synthetic biology and molecular breeding.