Our study aimed to discuss the correlation between microbial community succession and flavor formation during fast fermentation of three fish sauces, i.e., fermentation with Qu (FQ), insulation fermentation with Qu (IFQ) and insulation fermentation with enzyme (IFE), at the early (3M), middle (5M) and late (7M) stages. A total of 83 flavor compounds were identified in three samples, ethanol, 2-furanmethanol and 3,5-dimethyl-pyridine had the highest content in FQ sample, while oleic acid, decane and 2,5-octanedione were the key flavors in IFQ and IFE samples. During FQ fermentation, Halanaerobium was the predominant genus at the early stage, and its relative abundance declined gradually after 7M of fermentation. Halanaerobium, Staphylococcus and Lactobacillus were the dominant genera at 3M of IFE sample, but Tetragenococcus quickly occupied the dominant position after 7M. Acinetobacter played a dominant role during the fermentation of IFQ sample. Redundancy analysis showed that Tetragenococcus might promote the quality formation of IFQ and IFE, while Halanaerobium and Synechococcus led to the quality deterioration of FQ. Furthermore, Paenibacillus, Acetobacter, Lactobacillus, Tetragenococcus, Bacillus, Staphylococcus and Halanaerobium comprised the core microbiota responsible for the flavor generation in IFE group. These results provide new insights into the flavor formation of different fast-fermented fish sauces.