Bacillus anthracis, the causative agent of the deadly infectious disease anthrax, is also a typical biological warfare agent. It primarily infects livestock such as cattle and sheep, as well as humans, causing significant economic losses to the livestock industry and posing a threat to human society. A more profound insight into the genetic diversity and evolutionary drivers of this species is essential for studying its virulence mechanisms and conducting anthrax surveillance and control. However, current research in this area is insufficient, particularly lacking population genomic studies based on multiple types of genetic variation. In this study, we collect and filter the genome sequences of 1,628 publicly available B. anthracis strains, and identify various types of variation in 1,347 high-quality sequences, including SNPs, indels, large fragment gains and losses, copy number variations (CNVs), and genome rearrangements. In total, we identify 26,635 SNPs, 9,997 indels, 21 large fragment gains and losses, 25 CNVs, and 5 inversions. Phylogenetic reconstruction reveals that this species can be divided into six major populations and 17 subgroups. By integrating population diversity and geographic distribution characteristics, we find that U.S. strains exhibit the highest genetic diversity, while African strains show significant geographic clustering. Additionally, through selection pressure analysis, we identify strong selection signals in four genes (rpoB, fusA, spo0F, GBAA_RS11385) related to drug resistance and sporulation. This study reconstructs the global population structure of B. anthracis and reveals key variations during the species’ evolutionary process, providing targets for anthrax strain identification, tracing, and virulence mechanism research, as well as scientific support for the prevention and control of anthrax outbreaks.