With Bixiangzao and Mingfeng as experimental materials the chemical components of tea were determined by high performance liquid chromatography, and the microbial communities of fresh leaves and roots of different tea cultivars were analyzed by high throughput sequencing technology. The results included the predominant bacteria in the fresh leaves of Bixiangzao and Mingfeng tea were Proteobacteria, Bacteroidetes at the level of phylum and Chryseobacterium, Sphingomonas, Rhizobium, Methylobacterium and Aureimonas, etc. at the level of genus. The dominant bacteria in tea root were Proteobacteria, Actinobacteria and Firmicutes at the level of phylum, and Planococcaceae and Rhizobium and Sphingomonas at the level of genus. The abundance of endophytic bacteria in the leaves of Bixiangzao was higher than that of Mingfeng, while the abundance of endophytic bacteria in the roots of Mingfeng was higher than that of Bixiangzao. The diversity of endophytic bacteria in tea roots was higher than that in fresh tea leaves. The number of endophytic bacteria OTU in tea roots and leaves was less than that of soil microorganisms. Homology analysis showed that the endophytic bacteria mainly came from the leaf surface, while the root endophytic bacteria mainly came from the soil. The contents of theanine, amino acid, theobromine, caffeine, catechin, gallocatechin gallate, epigallocatechin gallate and maltose in fresh leaves of Mingfeng were significantly higher than those of Bixiangzao, while the contents of epigallocatechin, sucrose and phenolamine ratio in fresh leaves of Bixiangzao were significantly higher than those of Mingfeng. Correlation analysis showed that the numbers of some key bacteria genera were significantly positively or negatively correlated with the contents of some chemical components in tea, suggesting that different endophytic bacteria might be involved in the synthesis of quality components of tea trees, thus affecting the quality of tea.