The microbial community structure in Liupao tea at different stages of pile fermentation was studied by traditional microbial isolation and molecular identification. A total of 27 bacteria belonging to 13 genus, 8 actinomycetes species belonging to 7 genus, and 23 fungal species belonging to 11 genera were identified. Aspergillus niger, Aspergillus tubingensis, Blastobotrys adeninivorans and Bacillus spp. were found at all stages of the fermentation process. Totally 22 species of bacteria, 7 species of actinomycetes and 9 species of fungi were reported first in Liupao tea. These findings are helpful to understand the microbial role in the pile fermentation of Liupao tea, and provide a theoretical basis for the pure culture fermentation and microbial safety analysis of Liupao tea.