Abstract: In this study, pepper and tomato sour soup, the raw materials of red sour soup were taken as the research objects. Illumina MiSeq, total acid titration, gas chromatography-mass spectrometry and other equipment or methods are used to analyze the dynamic trend of microflora, total acid, pH value and volatile substances in the fermentation process of two kinds of sour soup. The results showed that Lactobacillus namurensis (27.67%) and Lactobacillus pentosus (41.75%) were the dominant lactic acid bacteria in pepper and tomato sour soup, respectively; Debaryomyces hansenii (76.05%, pepper sour soup) and Pichia membranifaciens (80.88%, tomato sour soup) were the dominant fungi in the later stage of fermentation. In terms of volatile substances, 156 and 92 compounds such as alcohols, ketones, aldehydes and esters were detected in pepper and tomato sour soup respectively. Among them, esters (24.99%), terpenes (20.21%) and ketones (17.60%) were several compounds with high content in chili acid soup in the early stage of fermentation; In tomato sour soup, aldehydes (41.30%) and ketones (20.28%) were the main compounds. With the change of fermentation, the main flavor compounds of chili acid soup were alcohols and esters, represented by linalool (10.43%) and ethyl hexadecanoate (12.12%); In tomato sour soup, alcohols, esters and phenols were the advantages. Among them, phenylethanol (31.93%) and 4-ethylphenol (8.71%) played an important role in the flavor of tomato sour soup. In general, the dominant functional microorganisms in the naturally fermented sour soup are Lactobacillus and yeast, and the total acid content higher than 25 g/kg can be obtained within 21~28 days after fermentation. The volatile substances vary greatly with the fermentation period. The relevant data can provide a reference for the development of directed vat set for sour soup and the optimization of processing technology.