<p><i>Anoectochilus roxburghii</i> is an endangered herb known for its functional substance, and light quality can significantly influence its growth and secondary metabolite content. However, the metabolic regulation mechanisms of <i>A. roxburghii</i> in response to light quality remain unclear. This study investigated the effects of different light qualities on the development and secondary metabolite synthesis in <i>A. roxburghii</i>, using blue light (B), red-to-blue light ratios of 1:2 (R1B2), 1:1 (R1B1), and 2:1 (R2B1), as well as red light (R) and white light (W) treatments. The R2B1 treatment notably increased the accumulation of phenolic acids and flavonoids, particularly kinsenoside, with levels 81.25% higher in leaves and 72.24% higher in stems compared to the W group. Transcriptome analysis revealed a reduction in polyamine levels and activation of phenylpropanoid, flavonoid, and kinsenoside biosynthetic pathways. Gene expression analysis also showed upregulation of genes related to photosynthesis and metabolite biosynthesis, suggesting that red-blue light promotes the production of functional metabolites in <i>A. roxburghii</i>. This research provides valuable insights into the metabolic regulation of <i>A. roxburghii</i> in response to light quality and offers strong scientific evidence to support its cultivation and production.</p> Graphical Abstract <p></p>