Campylobacter is an important zoonotic pathogen causing gastroenteritis worldwide, and poses a serious threat to public health. The complexity of prevalence, transmission, and diffusion is associated with high genomic variations of Campylobacter. Whole Genome Sequencing (WGS) is an efficient tool to identify species quickly and accurately, analyze the differences between different individual genomes, predict bacterial resistance, virulence genes and population evolution models on the genetic level. Here we review the application of the whole genome sequencing in Campylobacter genomic analysis to provide a basis for the prevalence and prevention of Campylobacter.