The major phytochemicals in the roots of Cudrania tricuspidata are prenylated xanthones, exhibiting significant structural diversity and bioactive properties, such as anti-inflammatory, antioxidative, and antitumor effects. The biosynthetic pathways of these compounds have not yet been resolved, limiting their production through synthetic biology. In this study, benzoyl-coenzyme A (CoA) ligase (BZL), benzophenone synthase (BPS), and benzophenone 3 '-hydroxylase (B3 ' H) transcripts involved in the biosynthesis of xanthone were cloned and characterized from C. tricuspidata. The results showed that C. tricuspidata BZL (CtBZL) catalyzed the formation of benzoyl-CoA from benzoate and C. tricuspidata BPS (CtBPS) catalyzed the condensation of benzoyl-CoA and three molecules of malonyl-CoA to form 2,4,6-trihydroxybenzophenone (2,4,6-triHB) via Claisen type cyclization. Then, C. tricuspidata B3 ' H (CtB3 ' H) hydroxylated 2,4,6-triHB to produce 2,3 ',4,6-tetrahydroxybenzophenone (2,3 ',4,6-tetraHB), which was a key precursor of xanthone derivatives. In addition, the functions of the enzymes were further explored by the heterologous expression of CtBZL, CtBPS, and CtB3 ' H in Saccharomyces cerevisiae and Nicotiana benthamiana. Also, a preliminary heterologous synthesis system of 2,3 ',4,6-tetraHB was established. The present study provided the candidate genes and strategies for the heterologous production of xanthones using S. cerevisiae and N. benthamiana as hosts.