Inflammatory bowel disease (IBD) is an idiopathic inflammatory disease with a high incidence. Multiple factors including dietary composition contribute to its occurrence. Recently, ketogenic diet which consists of a high proportion of fat and low carbohydrates has gained great popularity. Our study is aimed to explore the effect of ketogenic diet on IBD and its potential mechanisms. C57BL/6 mice were given a ketogenic diet or a control diet for a month and IBD was induced by 2% DSS in drinking water in the last week. Gut histology, inflammatory cytokines and chemokines, gut microbiota and metabolism were assessed. Ketogenic diet substantially worsened colitis, in terms of higher body weight loss, DAI scores and histological scores as well as colon length shortening. Levels of serum and colon inflammatory cytokines and chemokines (IL-1α, IL-6, TNF-α, IL-17, GM-CSF and IL-10) were significantly up-regulated in mice treated with ketogenic diet and DSS. Increased intestinal permeability and decreased expressions of intestinal epithelial barrier associated genes were observed due to ketogenic diet administration. Pretreatment with ketogenic diet alters the bacterial abundance, increasing pathogenic taxa such as Proteobacteria, Enterobacteriaceae, Helicobacter and Escherichia-Shigella and decreasing potential beneficial taxa such as Erysipelotrichaceae. Ketogenic diet also modified gut metabolism, increasing metabolites in the bile secretion such as ouabain, taurochenodeoxycholic acid, quinine, cholic acid and glycocholic acid, and decreasing metabolites associated with the biosynthesis of unsaturated fatty acids including stearic acid, arachidic acid, erucic acid, and docosanoic acid. These results suggest that ketogenic diet aggravates DSS-induced colitis in mice by increasing intestinal and systemic inflammation, and disrupting the intestinal barrier, which results from modulated gut microbiota and metabolism.