Dongcai is loved for its delicious flavor and nutritional value. The microorganisms in Dongcai play a vital role in their flavor, quality, and safety, and the microbial communities of Dongcai vary greatly from region to region. However, it remains unknown what the predominant microorganisms are in different traditional Dongcai and how they affect its flavor. The objective of this study is to explore the microbial diversity of traditional fermented Dongcai in three representative Chinese regions (Tianjin, Sichuan, and Guangzhou) and further assess their microbial functions. The microbial diversity of fermented Dongcai in Guangdong has the lowest diversity compared to fermented Dongcai in Sichuan, which has the highest. The distribution of the main genera of fermented Dongcai varies from region to region, butCarnimonas,Staphylococcus,Pseudomonas,Sphingomonas,Burkholderia-Caballeronia-Paraburkholderia,andRhodococcusare the dominant genera in common. In addition, halophilic bacteria (HAB, i.e.,Halomonas Bacillus,Virgibacillus, etc.) and lactic acid bacteria (LAB, i.e.,WeissellaandLactobacillus) are also highly abundant. Of these,Burkholderia-Caballeronia-Paraburkholderia,Rhodococcus,Sphingomonas,Ralstonia,andChromohalobacterare dominant in the Sichuan samples. In the Tianjin samples,Lactobacillus,Weissella,Virgibacillus,Enterobacter,Klebsiella,andPseudomonasare the most abundant. Predictions of microbial metabolic function reveal that carbohydrates, amino acids, polyketides, lipids, and other secondary metabolites are abundantly available for biosynthesis. In addition, the different flavors of the three types of Dongcai may be due to the fact that the abundance of HAB and LAB shows a significant positive correlation with the amounts of important metabolites (e.g., salt, acid, amino nitrogen, and sugar). These results contribute to our understanding of the link between the distinctive flavors of different types of Dongcai and the microorganisms they contain and will also provide a reference for the relationship between microbial communities and flavor substances in semi-fermented pickles.