In this study, four varieties of dried longan were used as the research materials, a genomic library of the microflora in dried longans was constructed by high-throughput sequencing technology. The community structure and abundance of microorganisms in longan’s flesh tissues were analyzed at various levels, and the diversity of microbial communities, and the correlation between the microbial community of dried longan samples and their characterized chemical indicators was analyzed. The results showed that the pectin content of the four varieties of dried longan ranged from 7.21 mg/g to 10.62 mg/g. The highest contents of vitamin C and total sugar were found in the Feng Li Sui longan variety, containing 4.25 mg/100 g and 116.89 mg/g, respectively. The titratable acid content was 0.061% for the Chu Liang longan variety, while the Thai and Feng Li Sui longan varieties had similar titratable acid content. The diversity analysis of microbial flora indicated the differences in the community composition and relative abundance of the microbial flora among the different varieties of dried longan. For example, the abundance of Proteobacteria was relatively high in the Thai and Feng Li Sui longans, accounting for 65.35% and 64.89% respectively, whilst Firmicutes was more abundant in the Mu Yan (51.36%) and Chu Liang (46.78%) longan samples. The correlation analysis showed that the moisture, vitamin C and sugar contents had greater effects on the diversity of microbial communities, whilst the level of titratable acid had a relatively small effect on the diversity and quantity of bacteria in the dried longan samples. This experiment provides an important reference basis for the selection of dried longan varieties for processing and storage, and offers a theoretical basis for the processing and quality control of dried longan products.