This study compared the effects of two sorghum varieties, glutinous sorghum (LS) and non-glutinous sorghum (FS), on the physicochemical properties, microbial communities, and metabolite composition during the fermentation of Zaopei in strong-flavor Baijiu production. The results showed that the LS sorghum type exhibited higher bacterial diversity and more complex microbial interaction networks compared with the FS type. In contrast, fungal communities showed stronger modularity and clearer functional differentiation. Significant differences were also observed in metabolite profiles between the two sorghum varieties, particularly in lipid metabolism. Glycerophospholipids were notably enriched in the LS group and were closely associated with key microbial genera involved in flavor formation. These compounds may contribute to the synthesis of important flavor esters and therefore influence the overall quality and aroma characteristics of Baijiu. Overall, the findings demonstrate that sorghum variety plays a crucial role in shaping microbial community structure, metabolic pathways, and flavor precursor formation during Baijiu fermentation. The study highlights that the selection of appropriate grain types is essential for optimizing Baijiu taste and quality, and future research should further investigate other grain-related parameters affecting fermentation and flavor development.