Lactobacillus helveticus, as a potential probiotic resource, is crucial for research on its gene functions and industrial development potential. However, studies on its genomic diversity and adaptive evolution characteristics remain inadequate. This study delves into the genomic characteristics, population structure, and functional diversity of L. helveticus by conducting a comparative genomics analysis of 187 strains [184 strains from NCBI, 3 isolates from dairy]. The results indicated that 187 L. helveticus genomes had a large and open pan-genome (14,047 pan-genes and 503 core genes). The coregene phylogenetic tree constructed from 187 L. helveticus genomes primarily divides into six clades, However, significant functional metabolic differences (P < 0.05) were observed between different clades and isolation sources, with the presence of unique CAZymes, such as enhanced mannose degradation (GH92) and intestinal starch degradation (GH13_14). Three dairy-associated isolates of L. helveticus were found genomic rearrangements. Additionally, various MGEs were identified (plasmids, IS, prophages, etc.), facilitating the dissemination of virulence factors like ClpP [VF0074] and HasC [VF0244]. These results underscore the remarkable genome and function diversity of L. helveticus, with MGEs driving the evolution of genomic diversity among strains. Our study offers fresh perspectives and strategies for selecting candidate strains for application in the food industry.