Flavonoids, as the main secondary metabolite in tea plant [Camellia sinensis (L.) O. Kuntze], shows decisive effects on the quality of tea and health functions. The tissue-specific synthesis and accumulation of flavonoids in tea plant were investigated by LC-TOF/MS and qRT-PCR. The result showed that phenolic acids, catechins, flavonols in different tissues and organs were abundant in the contents and diverse in the components, and the contents of proanthocyanidins were low. The components were rich in the leaves, while less in the roots. In term of gene expression, expression levels of 4CL, CHI, F3H and F3’5’H decreased in turn from the leaf, stem to the root. Enzymatic experiment showed there was no obvious difference in activities of DFR/LAR and ANR in the leaves and stems, while the weak activity of DFR/LAR was detected in the root. In leaves at different developmental stages, the content of catechin was the highest in the first leaf, followed by bud. The content of flavonol was high in the first and second leaf. The content of anthocyanin was reduced with the development of the leaves. The result of qRT-PCR showed that gene expression patterns of PAL, C4H, CHS, F3’H, F3'5'H, DFR, LAR and ANR were consistent with accumulation of catechins and flavonols in the leaves at different developmental stages. Enzymatic experiment showed that with the development of the fresh leaf, the activity of DFR/LAR reduced, in contrast, the activity of ANR increased gradually, which was consistent with trends of C and EGC accumulation.