[Background] Traditional fermented sweet paste has a delicious taste and unique flavor but little is known about microbial diversity during the fermentation by using high-throughput sequencing. [Objective] To analyze the microbial community structure and dynamic succession during natural fermentation of traditional sweet paste. [Methods] High-throughput sequencing was used to study the microbial diversity during natural fermentation of traditional sweet paste. [Results] In this study, 100 genera fungi and 432 genera bacteria were identified. Aspergillus is the dominant fungal species (≥76.96%) during the first 90 days of fermentation. Zygosaccharomyces is the dominant fungal species (≥85.42%) during 120 to 180 days of fermentation. Moreover, Bacillus is the primary bacterial genus (98.07%) during the first 43 h of fermentation and thereafter. In addition, the predominant bacteria in the koji and mash included Staphylococcus, Ralstonia, Pantoea, Burkholderia, Pediococcus, Sphingomonas, Bifidobacterium, Faecalibacterium, Kocuria and Lactobacillus. [Conclusion] The dominant florae of traditional sweet paste at different stages were determined. The results provide a theoretical basis for the study of the influence of different microorganisms on the flavor formation of the sweet paste.