Salmonella enterica serovar Enteritidis is one common foodborne pathogen that causes outbreaks. S. Enteritidis mainly causes gastrointestinal infections, whilst the invasive non-typhoidal Salmonellosis in sub-Saharan Africa are an increasing concern. Here, using multilevel genome typing (MGT) approach, we characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26,670 publicly available S. Enteritidis whole genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT level, globally prevalent and regionally restricted sequence types (STs) were identified; poultry associated MGT4-STs which were common in human cases in the USA were identified; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018, revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified MDR associated STs MGT for S. Enteritidis, which improves precision of detection and global tracking of MDR clones. The majority of the global S. Enteritidis population fell within two predominant lineages, which were found had significantly different propensity of causing large scale outbreaks, using the highest resolution level MGT9. Some virulence genes and Salmonella pathogenicity islands (SPIs) were found distributed differently in the MGT defined clades/lineages of S. Enteritidis. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.