The tea plant (Camellia sinensis (L.) O. Kuntze) is an important woody economic crop and often attacked by various insect pests such as tea aphids (Toxoptera aurantii Boyer de Fonscolombe). To reveal tea plant responses to tea aphid infestation, tea aphid-resistant cultivar ‘Taicha13’ and -susceptible one ‘Jingfeng’ were first screened, and then widely targeted metabolomics profiling, biochemical parameter and RT-qPCR analyses were performed in three samples, TCN (tea aphid non-infested ‘Taicha13’), JFN (tea aphid non-infested ‘Jingfeng’) and JFA (tea aphid-infested ‘Jingfeng’). The results showed amnio acid (plus proline) and protein content, and amnio acid: sucrose ratio were significantly less abundant in TCN relative to JFN, suggesting TCN is low nutritional quality for tea aphids. Metabolite profiling revealed that flavonoids and JA-isoleucine (JA-Ile) were more enriched in TCN and JFA compared to JFN, proposing effective roles of flavonoids and JA-Ile in tea plant defense against tea aphid infestation. RT-qPCR results demonstrated that five JA biosynthesis genes (CsLOX2, CsLOX3, CsOPR, CsAOC and CsJAR) in exception of CsAOS, and six flavonoid biosynthesis genes (CsPAL, CsC4H, CsCHS1, CsCHS2, CsFL and CsDFR) shared similarly higher abundance in TCN than in JFN, and exhibited elevated expression levels in JFA relative to JFN, further suggesting flavonoids and JA confer tea plant resistance against tea aphid feeding. Overall, our findings uncovered that tea aphid-infestation activated defensive responses and highlighted involvement of nutritional quality, flavonoids and JA-Ile in tea plant resistance against tea aphid infestation.