Salmonella enterica serovar Enteritidis is a common foodborne pathogen causing both invasive and non-invasive infections. Multilevel genome typing (MGT) is a recently developed novel hierarchical genome typing approach. In this study, a MGT framework for S. Enteritidis was established, including 9 multi-locus sequence typing (MLST) schemes of different resolutions, composed of increasing numbers of genes (from seven genes for MGT1 to 4986 genes for MGT9). MGT1 refers to the seven house-keeping genes MLST of Salmonella which is of the lowest resolution. A total of 26,670 publicly available genomes from 89 countries were analyzed with MGT. As the MGT levels grow, numbers of recognised sequence types (STs) increase in size from 252 STs by MGT2 to 20,153 STs by MGT9. STs at each MGT level were further grouped into clonal complexes (CCs) when STs differed by atmost one allele. Using CCs at the middle-resolution level of MGT4, CCs prevalent in all continents as well as CCs restricted to a single continent were found. Two CCs were common in all continents representing global epidemic lineages, with one CC more prevalent in North America and Europe. These two CCs, which included 87.5% of all S. Enteritidis isolates, were found to have different potential to cause outbreaks according to the number of highly similar clusters defined by MGT9. We also identified two CCs at MGT4 that contained exclusively the invasive S. Enteritidis strains prevalent in Africa. By analyzing the presence of virulence and multi-drug resistance genes, MGT of various resolution levels were able to identify unique clades of S. Enteritidis strains that harbored different virulence associated loci, such as the Yersinia high pathogenicity island (HPI), type VI secretion system, and multi-drug resistance genes. In conclusion, MGT of S. Enteritidis is a hierarchical, simple and stable method for the epidemiological surveillance of S. Enteritidis, which enables additional insights into the diversity and convergence of the virulence and multi-drug resistance of different clones.