BackgroundMicrobial community plays a crucial role in Chinese strong‐flavour baijiu (SFB) fermentation. However, the seasonal dynamics of the microbial community in the SFB fermentation system and its contribution to the unique flavor of SFB have not been fully elucidated. In this study, we investigated the seasonal dynamics of the microbial community through 16S rRNA and ITS gene sequencing.ResultsOur results revealed significant temporal dynamics of microbial communities and environmental variables throughout the four seasons. We found that the influence of seasons on fungal communities was more significant than that on bacterial communities. The diversity of bacteria exhibited higher levels during the winter and summer, whereas fungal diversity was more prominent in summer and autumn. Furthermore, while stochastic processes maintained their dominance in microbial assembly throughout all four seasons, the significance of heterogeneous selection increased during summer for both bacteria and fungi, while homogeneous selection became more pronounced during winter for fungi. pH and environmental temperature were important drivers of microbial community assembly across different seasons, primarily impacting the core genera responsible for the production of major volatile flavor compounds (VFCs), especially ethyl caproate.ConclusionThese findings provide new insights into the impact of seasons on microbial communities and hold promise for improving the quality control measures for SFB brewed in different seasons.This article is protected by copyright. All rights reserved.