Abstract: The changes of microbial community in the fermentation process of Yongchun aged vinegar are of great significance to its quality formation and process optimization. In this paper, the microbial screening, morphological identification and molecular biology preliminary identification were carried out on the fermentation samples of Yongchun aged vinegar. A total of 107 strains were screened, and most of them were identified as Bacillus, Acetobacterium Balch, lactic acid bacteria, Saccharomyces and Aspergillus. The high-throughput sequencing technology was used to analyze the bacterial and fungal diversity of the samples, and the microbial community structure was analyzed at different levels. In the composition of bacterial colonies, YCV1 (mother of vinegar) and YCV4 (2.5 years vinegar) were similar in composition, YCV2 (8 months vinegar), YCV3 (3 years vinegar) and YCV5 (1.5 years vinegar) were similar in composition, and YCZ1 (bed 1) and YCZ2 (bed 2) were similar in composition. HYQ1 (Heiyiqu) was significantly different from other samples. In the compositional analysis of fungal colonies, YCV2 and YCV3 were similar in composition, YCV4 and YCV5 were similar to YCZ2 to a certain extent, and YCV1, HYQ1 and YCZ1 were significantly different from other samples. The structure of fungal and bacterial colonies varied greatly in different samples. The research results provided scientific basis for the theoretical research and industrial production of Yongchun vinegar fermentation process, and could also lay a foundation for the later medicine-food homologous development of Yongchun vinegar.