Baishouwu (Cynanchum auriculatum), a medicinal and food dual-use plant, has been cultivated for centuries and is favored by consumers. C. auriculatum tuberous roots contain large amounts of avonoids, lignin, and other nutrients. However, the developmental characteristics and phenylpropanoid metabolic mechanism in C. auriculatum have not been clari ed. Here, C. auriculatum tuberous roots were observed in three developmental stages, compared with root forming stage (S1), there were signi cant morphological differences in root expanding stage (S2) and harvest stage (S3). Through Illumina HiSeq2500, nine transcriptomic libraries were constructed for transcriptomic analysis. 28,926 DEGs were activated during the development of C. auriculatum tuberous root, and many DEGs were enriched in 'phytohormone signal transduction' and 'phenylpropanoid biosynthesis'. The analysis of phytohormone content and gene expression revealed that, auxin, cytokinin, and ethylene participated in the regulation of C. auriculatum tuberous root development. With phloroglucinol staining, it was observed that ligni ed cells were mainly distributed in the central xylem at S1, followed by ring-like structure formation in S2, and nally formed the connecting rays between the xylem and the phloem in S3. Lignin content increased at S2 and then decreased at S3, and the expression of lignin synthesis genes also presented a similar trend. Total avonoids content showed a gradually increasing trend, and the expression of avonoid synthesis genes was also gradually up regulated. C. auriculatum might divert the precursors to the avonoid synthesis pathway by reducing the activity of key enzymes in lignin synthesis, resulting in the reduction of lignin content and the promotion of avonoid synthesis. This study provided a basis for the developmental mechanism of C. auriculatum and the further utilization of C. auriculatum tuberous roots.