Lactococcus lactis, a major starter culture in the dairy industry, has been widely applied in food fermentation. While current research has primarily focused on evaluating its role during fermentation, genomic investigations into its genetic diversity and functional adaptability remain limited. In this study, 199 L. lactis strains isolated from Chinese traditional artisanal cheeses (72 bovine, 71 goat, and 56 yak milk cheese isolates) were subjected to comparative genomic analysis. Genomic characteristic analysis indicated that bovine milk strains possess larger genomes and the highest number of unique genes. Functional characterization further demonstrated notable differences in carbohydrate metabolism among strains from different sources, with yak milk strains enriched in enzymes involved in complex polysaccharide degradation, including members of the carbohydrate esterases family. Moreover, strains from different sources exhibit distinct strategies for lactose hydrolysis and metabolic utilization, reflecting adaptive evolution to their specific nutritional niches. Analysis of the antibiotic resistance profile suggests that L. lactis predominantly harbors glycopeptide and lincosamide resistance genes, encompassing four distinct resistance mechanisms. Collectively, this study reveals the genetic diversity and adaptive evolution of L. lactis strains from different sources and identifies key genes associated with carbohydrate degradation, lactose metabolism, and antibiotic resistance, providing concrete genetic evidence for the selection of efficient and safe industrial fermentation strains.