In this study, 12 strains of Akkermansia muciniphila were isolated and characterized from healthy volunteers from different regions of Xinjiang Uygur Autonomous Region, China. Through whole-genome phylogenetic analysis, the genetic differences among these strains were compared. Their genome sizes ranged from 2.64 to 2.98 Mb, with GC contents between 55.1% and 55.7%. According to the phylogenetic tree constructed based on average nucleotide identity (ANI) and core genes, we categorized all isolates into three distinct subgroups. The results indicated that subgroup Ⅱ exhibited the highest acid and bile salt tolerance, with aggregation rates > 60% after 48 h and hydrophobicity of (32.00 ± 0.02)% after 15 min. This subgroup also had superior radical scavenging capacity against 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) cation radical. Hemolysis assays showed no significant hemolytic rings, indicating that all strains were safe for short-term usage. All strains were resistant to aminoglycoside antibiotics (streptomycin and gentamicin) and susceptible to glycopeptide antibiotics (vancomycin). The antibiotic resistance phenotype results were not completely consistent with the gene detection results. Genomic sequencing identified the glycoside hydrolase families 2 (GH2) and 20 (GH20). Carbon source utilization analyses indicated that galactooligosaccharides, soybean oligosaccharides, and xylitol synergistically promoted the proliferation of A. muciniphila. Taken together, subgroup Ⅱ strains exhibit great potential for use as probiotics.