Background Modern studies have shown that chrysanthemum has anti-inflammatory, regulating intestinal function and other effects, chrysanthemum stem and leaf as a nonmedicinal part of chrysanthemum, has similar chemical components with chrysanthemum, so it is speculated that chrysanthemum stem and leaf also has the effect of regulating intestinal inflammation. The purpose of this study was to evaluate the antiinflammatory and antioxidant effect of chrysanthemum stem and leaf extract through zebrafish inflammatory bowel disease model, and to detect flavonoids, phenolic acids and polysaccharides in chrysanthemum stem and leaf extract. Methods DSS induced inflammatory bowel disease model of zebrafish was used. Aliciin blue staining was used to observe the secretion of intestinal acid mucin, and H&E staining was used to detect the inflammatory cell infiltration. Superoxide dismutase activity was determined by kit, and the expression levels of key inflammatory cytokines IL-1 β , IL8 and MMP9 were detected by quantitative polymerase chain reaction. Furthermore, UPLC-TQ /MS method was used to detect the contents of flavonoids and phenolic acids in chrysanthemum stem and leaf extracts. Neutral and acidic polysaccharides were determined by the phenol-sulfuric acid method and the carbazol-sulfuric acid method. Results H&E staining showed that extracts from chrysanthemum stem and leaf inhibited inflammatory cell infiltration to varying degrees. The expressions of inflammatory cytokines IL-1 β , IL8 and MMP9 were significantly increased in DSS induced zebrafish. The extracts inhibited the expression of IL-1 β , IL8 and MMP9 in DSS induced zebrafish. The water extract 0.2mg/ mL and alcohol extract 0.04mg/ mL had the most significant inhibition. Superoxide dismutase activity in extract treatment group was also up-regulated compared with model group. The results showed that the contents of total flavonoids and phenolic acids in the alcohol extract of chrysanthemum stem and leaf were significantly higher than those in the water extract of chrysanthemum stem and leaf, but the water-soluble polysaccharides were significantly more in the water extract of chrysanthemum stem and leaf. Conclusions In conclusion, this study suggests that chrysanthemum stem and leaf extract can improve inflammatory bowel disease of zebrafish through antiinflammatory and antioxidant activities.