Strong flavour Baijiu is widely consumed in China and is produced by the fermentation of grains using microbial starters. However, a comprehensive understanding of the diversity and metabolic characteristics of microbial communities involved in the solid-state fermentation of Baijiu is important for determining the relationship between microbial composition, flavour metabolism and understanding Baijiu fermentation conditions. Although studies have examined the metabolic pathways and impact of major processes on flavour compounds in strong flavour Baijiu, aspects of the fermentation process remain unexplored. In this review, methods are discussed for the optimisation of microbial diversity in strong flavour Baijiu and associated effects on the flavour of Baijiu. Recent studies are reviewed on starters (Daqu), fermented grains (Jiupei), and pit mud together with the effects of microbial composition on the quality of strong flavour Baijiu. The challenges of Baijiu research and production are discussed, including the role of the microbial diversity of Daqu and Jiupei in the flavour composition of strong flavour Baijiu. This review contributes to the current understanding of processing strong flavour Baijiu and serves as a reference for screening flavour related microorganisms, which is valuable for improving the quality of strong flavour Baijiu.