Abstract: The bacterial diversity and metabolomic characteristics of yogurt from Xinjiang Bole were analyzed using Illumina sequencing and untargeted metabolomics, and the relationships between them were explored. According to the bacterial diversity analysis, the main bacterial genera in Xinjiang Bole yogurt include Lactobacillus, Klebsiella, Lactococcus, Acetobacter, among others. Using LEfSe and PICRUSt analysis, Lactobacillus, Klebsiella, and Lactococcus were identified as biomarkers, and their functions were predicted. The metabolomics analysis identified a total of 397 and 324 metabolites in positive and negative ion modes, respectively. The predominant categories of compounds identified were lipids and lipid-like substances, organic acids and their derivatives, and organic heterocyclic compounds. Notably, lipids and lipid-like substances, as well as organic acids and their derivatives, were the primary differential metabolites, significantly influencing the flavor of yogurt. The metabolic pathway analysis revealed amino acid metabolism and secondary metabolism as the main enriched pathways, which aligned partially with the functional prediction results. The integrated analysis of the microbiome and metabolome showed significant correlations between the genera Lactobacillus, Limosilactobacillus, Lactococcus, and Klebsiella and the metabolites of organic acids and their derivatives, as well as lipids and lipid-like substances, indicating that the microbial community affects the nutrients of yogurt through its metabolic activities. This study investigated the microbial community structure and metabolic products of three distinct types of yogurt from Bole, Xinjiang, aiming to provide a scientific theoretical basis for the production and quality improvement of Xinjiang yogurt.