Abstract: The content changes of chemical components in different phenological phase of the cultivated Polygala tenuifolia is one of the important factors for determination of the best harvest time in the production practice. In this study, the digital gene expression (DGE) profiles of the cultivated P. tenuifolia were analyzed in different phenological phase (flowering fruit bearing stage, wilting stage, dormancy stage). The differentially expressed genes were found in the biosynthesis of chemical composition in P. tenuifolia, and the representational ones were validated by RT-qPCR. Then, the key enzymes (CYP450s and UGTs) involved in the downstream of the triterpenoid saponins biosynthesis pathway in P. tenuifolia were predicted through the correlation analysis of gene expression. The number of down-regulated genes was more than that of up-regulated in P. tenuifolia from flowering fruit bearing stage to dormancy stage. Six differentially expressed genes (HMGS, PMK, FPPS, SQS, SE, β-AS) and five (PAL, C4H, 4CL, CAD, peroxidase) were annotated to the triterpenoid saponins and phenylpropanoid biosynthesis pathway in P. tenuifolia, respectively. Compared to wilting and dormancy stages, the saponins, xanthones, and lignins were largely synthesized at the flowering fruit bearing stage of P. tenuifolia. Furthermore, UGT83A1, CYP716B1, CYP98A3, CYP86B1, and CYP94A1 may be the part of key enzymes in the downstream of the triterpenoid saponins biosynthesis pathway in P. tenuifolia. This study provides evidence to support the correctness of traditional harvest time of P. tenuifolia at the level of transcription, and lays the scientific foundation for gene cloning and functional verification of CYP450s and UGTs in the downstream of the triterpenoid saponins biosynthesis pathway in P. tenuifolia in the future.