In recent years, using genetic engineering and bioengineering techniques, Bifidobacterium as a carrier to express specific functions of the protein or polypeptide, has become a new treatment for disease. Ulcerative colitis (UC) is a type of inflammatory bowel diseases (IBD). Although the cause of this inflammatory disorder is still unknown, a large amount of evidence suggests that ulcerative colitis is associated with increased activity of reactive oxygen species (ROS), manganese superoxide dismutase (MnSOD) is a kind of superoxide dismutase (SOD) has been demonstrated to play a key role in the pathophysiology of colitis. Here, we explored the Bifidobacterium as a drug delivery system to orally deliver a potent anti-inflammatory but poor penetration and stability antioxidant enzymes human MnSOD, transported into cells by a penetratin PEP-1. We constructed an expression vector expressing PEP-1-hMnSOD fusion protein, and successfully expressed hMnSOD fusion protein in engineered Bifidobacterium. Then we identified the bioactivity of engineered Bifidobacterium in LPS-induced inflammatory cell model. Finally, we used Bifidobacterium expressing PEP-1-hMnSOD fusion protein against DSS-induced ulcerative colitis mice. B. longum-PEP-1-rhMnSOD can successfully express rhMnSOD in the colon. We found that levels of inflammatory cytokines TNF-α, IL-1β, IL-6 and IL-8 as well as histological damage in colonic tissues showed that engineered Bifidobacterium effectively reduced dextran sulfate sodium(DSS)-induced ulcerative colitis, we also tested the MPO, verified the above conclusions. These results suggest that oral Bifidobacterium expressing PEP-1-hMnSOD fusion protein can be treated as a new method of UC treatment.