Plant metabolites such as tea polyphenols, theanine, with extensive health benefits, are extremely rich in tea tree. Flavonoids are the main component of tea polyphenols, while glutamine is the precursor substance of the synthesis of theanine. This study attempted to elucidate the related genes of the metabolisms of tea polyphenols and theanine of Jing’an white tea. Fresh buds and leaves of Camellia sinensis cultivar Jing’anbaicha were selected as samples, the transcriptome was constructed using Illumina HiSeqTM 4000 sequencing technique and the data were analyzed using the bioinformatics methods subsequently. 100568 unigene sequences were obtained with length of 95121064 bp. Gene function annotations analysis showed that 32530 annotations were acquired from Nr database, 30087 annotations were acquired from KOG database, 29010 annotations were acquired from GO database, 24553 annotations were acquired from Swiss-Prot database, 18576 annotations were acquired from Pfam database, respectively. The key differences unigene sequences related to the metabolic pathway of flavonoids and glutathione in Jing’an white tea buds and leaves were explored through the GO analysis and the KEGG metabolic pathway analysis. This study could provide references for further study of the biosynthesis regulation of tea polyphenols and theanine in Jing’an white tea.