Many studies have shown that phenolic compounds such as lignin and flavonoids enhance plant resistance. Tea plants are rich in flavonoid compounds. Whether these compounds are related to tea plant resistance is unclear. In this study, an interesting conclusion was drawn on the basis of experimental results: in response to abiotic stress (except for sucrose treatment), gene expression was increased in the phenylpropanoid and lignin pathways and was reduced in the flavonoid pathway in tea plants. CsHCTs, the genes located at the branch point of the lignin and flavonoid pathways, are most suitable for regulating the ratio of carbon flow in the lignin pathway and flavonoid synthesis. Enzymatic and genetic modification experiments proved that CsHCTs encode hydroxycinnamoyl-coenzyme A:shikimate/quinate hydroxycinnamoyl transferase in vitro and in vivo. Furthermore, the genetic modification results showed that the contents of phenolic acids and lignin were increased in tobacco and Arabidopsis plants overexpressing CsHCTs, whereas the content of flavonol glycosides was decreased. Both types of transgenic plants showed resistance to many abiotic stresses and bacterial infections. We speculate that CsHCTs participate in regulation of the metabolic flow of carbon from the flavonoid pathway to the chlorogenic acid, caffeoylshikimic acid, and lignin pathways to increase resistance to biotic and abiotic stresses.