We performed full-length transcriptomic analyses to identify candidate genes involved in the biosynthesis pathway of triterpenoid saponins of Polygala tenuifolia Willd. These results were beneficial for enriching the gene resources of Polygala tenuifolia and discovering candidate genes related to the synthesis of medicinal ingredients. By intervening in gene expression at the gene level, the accumulation of medicinal ingredients can be improved, which was of great value for the sustainable utilization of Polygala tenuifolia medicinal resources. This study also layed a certain foundation for genetic engineering of triterpenoid biological pathways in Polygala tenuifolia in the future.