Medicarpin, a potent bioactive compound found in plants like Sophora japonica and Glycyrrhiza species, exhibits diverse medicinal properties. Despite limited natural plant sources and low yields, this study identified eight key genes governing medicarpin biosynthesis. Through genetic engineering in Saccharomyces cerevisiae using liquiritigenin as a substrate, the team achieved medicarpin production at 0.82 ± 0.18 mg/L. Gene copy enhancements of vestitone reductase (VR) and pterocarpan synthase (PTS) boosted yields to 2.05 ± 0.72 mg/L. This research lays a robust foundation for economically viable and sustainable synthetic production of medicarpin via a synthetic biology approach.