As the main components in tea flowers, catechins are accumulated at each stage of tea flowering. However, little information on the accumulation mechanism of catechins during tea flowering is available. Here, we analyzed the accumulation of catechins in tea flowers as well as the expressions of related genes during tea flowering. The results indicated that 99 unigenes and 269 transcription factors (TFs) were assigned to the flavonoid biosynthesis pathway, and the contents of catechins differed significantly at different flowering stages, except for epigallocatechin. A holistic analysis between the contents of catechins and the expressions of catechin-related genes suggested that phenylalanine ammonia lyase (PAL1, Unigene23632), 4-coumaroyl-CoA ligase (4CL1, Unigene40857), chalcone synthase (CHS2, CL5310.Contig3), flavonoid 3′-hydroxylase (F3′H1, CL491.Contig2), and flavonol synthase (FLS, Unigene33148) were the critical genes in regulating the biosynthesis of catechins. Thereinto, the CHS2 and FLS that highly expressed at the early flowering stage showed positive correlations with the contents of catechin, epigallocatechin gallate, epicatechin gallate, and total catechins. In addition, the 4CL1, F3′H1, and PAL1 that highly expressed at later flowering stage showed negative correlations with the contents of total catechins. Moreover, the MYB, bHLH, NAC, WRKY, and MADS could be the major TFs implicated in the biosynthesis of catechins in tea flowers. Among them, MYB44, WRKY7, and WRKY17 were special TFs regulating catechins biosynthesis in tea flowering. Overall, this study first described the function of genes related to catechins biosynthesis in tea flowers, and the data may serve as valuable resources for studying the molecular mechanisms of catechins biosynthesis during tea flowering.