Abstract <p>White clover (<i>Trifolium repens</i> L.) is an important lawngrass of good quality. Sequence transcriptome analysis was performed at the vegetative and flowering stages using high-throughput sequencing technology to investigate the genetic basis of secondary metabolite synthesis in white clover. The results showed that the number of upregulated genes increased significantly in the flowering stage compared to the vegetative stage. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and transcriptome analyses, we found that flavonoid and terpenoid synthesis pathways affected the growth and development of white clover. Expression of the DXP terpenoid synthesis pathway was higher at the vegetative stage than at the flowering stage. Analysis of the major pathways of flavonoid synthesis showed that the expression of flavonoid synthesis genes significantly increased at the flowering stage. To further verify the function of <i>CHS</i>, a key gene in the flavonoid synthesis pathway, we carried out a transgenic analysis of <i>CHS</i> in white clover. This study showed that <i>CHS</i> gene expression and flavonoid content significantly increased in transgenic tobacco. These results provide a solid theoretical basis for future research on the growth and development of white clover and breeding.</p>