The microbial composition and environmental factors can take a great influence on community succession during the solid-state fermentation (SSF) of Maotai-flavor Baijiu. In this paper, high-throughput sequencing was used to reveal the dominant microorganisms and the evolution process of microbial community structure in the initial fermentation of Maotai-flavor Baijiu. The correlation analysis was carried out for the relationship between physicochemical factors and fermented microbes. The results showed that microorganisms were obviously enriched and the diversity of bacteria and fungi showed a downward trend during the heap fermentation process of Maotai-flavor Baijiu. However, the diversity of fungi in the pit fermentation process increased. Generally, Lactobacillus, Pichia, and Saccharomyces were the dominant microorganisms in the initial fermentation of Maotai-flavor Baijiu. According to the redundancy analysis, we found that reducing sugar was the key driving factor for microbial succession in the heap fermentation, while acidity, alcohol, and temperature were the main driving forces in pit fermentation. This study revealed the microbial succession and its related environmental factors in the initial fermentation of Maotai-flavor Baijiu, which will enrich our knowledge of the mechanism of solid-state liquor fermentation.