Objectives Escherichia coli Nissle 1917 (EcN) was used to express antimicrobial immune peptide Scygonadin (Scy) and the effects of EcN-Scy on alleviating colitis were evaluated to provide theoretical basis for the development of novel substitutes for antibiotic. Methods The vector pnirBMisl (pnir) and the target gene of antimicrobial peptide Scy were amplified with PCR, and the recombinant vector EcN-Scy was obtained by homologous recombination connection. Twenty 8-week-old female BALB/c mice were randomly divided into four groups including the control group, DSS group, DSS+EcN group, and DSS+EcN Scy group. The mice were orally administered with PBS, EcN bacterial solution, or EcN-Scy bacterial solution every 2 days and their body weight was recorded. The experiment lasted for 14 days. Except for the control group, the other three groups were induced colitis by adding 3% DSS to their drinking water from day 0 to day 7. Mice were killed on day 14 after anesthesia, and samples of serum and colon tissue were collected for testing. Results EcN-Scy treatment significantly alleviated the weight loss in mice (P<0.05) and the symptoms of colon shortening caused by DSS (P<0.05), and significantly improved the structure of colonic villi compared with DSS group. The level of ALP and Urea in serum in the DSS+EcN-Scy group was significantly increased by 28.6 U/L and 1.35 mol/L (P<0.05) compared with that in DSS group. The level of TBil and LDH had a decreasing trend (P>0.05). The level of pro-inflammatory cytokines TNF-α, MCP1, and IL-1 β in the serum of the DSS+EcN-Scy group was significantly reduced by 18.9%, 50.9%, and 8.9%, respectively (P<0.05), and the level of MCP1 and IL-6 in the colon were reduced by 40.4% and 21.9%, respectively (P<0.05) compared with that in the DSS group. Conclusions The antimicrobial immune peptide Scy was successfully expressed with the engineered bacterium EcN, which has a significant effect on alleviating colitis in mice. It can improve the weight loss, colon shortening, and morphological damages in mice induced by DSS, and reduce the level of inflammatory factors in serum and colon.