Abstract: The basic helix–loop–helix (bHLH) transcription factor family, the second largest class of transcription factors in plants, plays a central role in the regulation of plant growth, development, and responses to environmental stresses. With the rapid advancement of high-throughput sequencing and genomic technologies, studies on bHLH family members in woody plants have progressed considerably, particularly with respect to gene structure, phylogenetic relationships, and functional characterization. In this review, we systematically summarized the structural features of the bHLH gene family and comprehensively elucidated its regulatory roles in woody plant growth and development, secondary metabolite accumulation, and anthocyanin biosynthesis. Building on this foundation, we further explored the potential applications of bHLH transcription factors in germplasm innovation and genetic improvement of woody species. A more in-depth dissection of the regulatory networks mediated by bHLH transcription factors will provide critical theoretical insights and valuable genetic resources for the improvement of key traits and germplasm innovation in woody plants.