Solid-state fermentation is a dynamic process involved with complex microbiome. Microbial structure and succession significantly affect the yield and quality of fermentation productions. Although the importance of microbial structure was extensively studied, the significance of microbial succession rate remains unclear in solid-state fermentation. To address this gap, we designed an in situ experiment in a typical distillery to characterize the effects of microbial succession rate. In this study, we found the process of strong-aroma Baijiu making could be divided into two stages according to fermentation parameters (starch, moisture, acidity, reducing sugar, alcohol, temperature). The early stage showed significantly (p < 0.05) higher microbial diversity than that of the later stage according to Shannon index. Compared with single cereal fermentation, mixed cereals fermentation showed slower microbial succession rate of stage shift. We found that Lactobacillus could reflect microbial succession rate of stage shift in strong-aroma Baijiu fermentation. Meanwhile, we found fermentation parameters could affect microbial succession rate of stage shift. Microbial diversity was significantly (p < 0.05) correlated with fermentation parameters. Moreover, molecular ecological network analysis (MENA) showed that succession rate of microbial community could affect microbial interactions. In addition, fermentation of mix cereals (sorghum, wheat, corn, rice and glutinous rice) increased the enrichment of Clostridiales from pit mud according to results of source tracking. Collectively, succession rate of microbial community could be an important trait to explain differences of microbial diversity and flavor profile from the perspective of microbial decline and enrichment. Our study highlighted the importance of microbial succession rate during strong-aroma Baijiu making process and provided a dynamic perspective to observe solid-state fermentation.