High-throughput sequencing (HTS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) were used to compare the microbiota structure and metabolic compounds of traditional suancai from Heilongjiang (HLJ), Shanxi (SX) and Qinghai (QH) in China. Besides, the physicochemical properties such as total number of colonies, pH and total acid content were determined, and the related factors of the differences were analyzed. The salinity of the 3 samples was 1.9%, 8.0% and 10.0%, respectively, and the dominant bacterial genera were Loigolactobacillus, Arcobacter, and Marinomonas. Meanwhile, Loigolactobacillus was significantly positively associated with pH and nitrite in HLJ, Arcobacter was inversely related to pH and nitrite, while Marinomonas was negatively correlated with all physicochemical properties in QH which had the highest salinity. In addition, the 5 main differential metabolites in the 3 samples were acetic acid, 4-ethylphenol, 2,2,4-trimethyl-1,3-pentanediol diisobutyrate, 2,4-tert-butylphenol, and 3-butenenitrile. Among them, the ketones and acids were positively correlated with the core bacteria in HLJ with the lowest salinity, and the main genera in SX were positively associated with various alcohols, while there was a positive correlation between Marinomonas and butyronitrile alcohol in QH with the highest salinity. This study provided a guidance for the differences and correlations of microorganisms, flavor compounds, and quality characteristics from a regional perspective by studying the various quality characteristics of the suancai.