There is limited information on the chemical components and microbiota changes involved in da-jiang, a Chinese popular traditional fermented soybean condiment. Therefore, dynamic changes both in physicochemical quality and microbial community diversity of 20 samples of naturally fermented da-jiang collected over 95 days were measured, and we classified the samples into 5 groups (each containing 4 time points) according to the results. Based on OTUs analysis, Group 2 and Group 3 might represent the shift-stage between bacteria and fungi. Also, our results demonstrated that the formation of flavour, nutrient and quality of the traditional da-jiang were actually related to all of microbial community, especially the increased bacteria, including Staphylococcus and Leuconostoc. Correspondingly, ‘Membrane Transport’, ‘Carbohydrate Metabolism’, ‘Amino Acid Metabolism’ and ‘Replication and Repair’ were the top 4 KEGG pathways based on bacterial genes. The findings are expected to be helpful for us not only to understand the formation of flavour, taste and quality of traditional fermented da-jiang, but also to improve the industrialised fermented da-jiang.