Ulcerative colitis (UC) is a recurrent chronic inflammation of the colon with increasing incidence and prevalence, which could increase the risk of colorectal cancer. It is urgent to find an effective method with few side effects. Nanocrystalline cellulose (NCC), which is from plant fibers, has a good biocompatibility and high biosafety. Herein, we used NCC to treat UC and evaluated its treatment effect by the disease activity index, intestinal pathology, inflammatory cytokines, tight junction proteins, and mucins. We studied the impact of NCC on mucin expression and gut microbiota to discuss the therapeutic mechanism. NCC can effectively treat UC by regulating the MAPK pathway of mucin 2 and the relative abundance of Akkermansia and Odoribacter, which could not cause the body damage. NCC could not cause body damage compared to the medications, while it had a better effect on the regulation of MUC2 compared to the present drug substitutes. NCC is a practical alternative for the treatment of UC.