Background: Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses severe threat to public health. Chicken meat and egg are the main source of SE. DNA methylation, an important epigenetic modification, involves in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole genome bisulfite sequencing in the current study. Results: There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean Reads, 126,782,896 unique reads in the inoculated group. We found that the methylation density in gene body was higher than that in the upstream and downstream regions of gene. There were 8,946 differentially methylated genes (3,639 hypo-methylated genes, 5,307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated and mainly distributed in Chr2 and 7. Conclusions: We firstly analyzed the genome-wide DNA methylation in the response to SE inoculation in chicken. SE inoculation promoted the DNA methylation in chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play a crucial role in the methylation regulation of SE infection in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.