Chinese Strong-flavor Baijiu (CSFB) is a traditional Chinese fermented beverage with sales accounting for more than 70% of total Baijiu consumption in China. CSFB is produced by fermentation of grains in cellars lined with pit mud (PM). This PM, fermented clay, contains large amounts of functional microbes, which are of great importance in determining the production of aromatic compounds in CSFB. Because of this key role, many researches have been conducted in recent years to study the effect of PM microbial mechanisms on the CSFB production. In the present paper, we introduced the recent advances in research on the diversity and succession of PM microbial community, the relationship between microbial community structure and PM quality, and the breeding and application of PM functional microbes. Then, the main associated issues were analyzed and the research prospects were put forward. Firstly, the comparative study on PM microbial community structure should be developed to illustrate the relation between microbial community structure and CSFB quality, and improve the PM quality appraisal system. Secondly, the isolation and improvement of functional strains should be enhanced, and the metabolic pathways and its influence mechanism of isolates should be demonstrated to promote the potential application of PM microbes. Finally, the detail affecting function of microbial agents used in the manufacture of artificial PM should be investigated. When the mechanisms of complex microbial agents were demonstrated in the aspects of microbial community structure and metabolism, quality control on the microbial agents could be promoted.