Due to the insolubility of phytosterols in both water and oil, their application in the medicine and health and food industries is limited. In this study, zein and pectin were selected as wall materials of phytosterol nanoparticles to enhance the solubility and bioactivity of phytosterols. The colitis-inhibitory effects of zein-based stigmasterol nanodispersions (ZNs) and zein/pectin-based stigmasterol nanodispersions (ZPNs) were investigated in the sodium dextran sulfate (DSS)-induced colitis mouse model. The results showed that ZPNs’ therapeutic effect was better than that of ZNs. According to electron microscopy observation, pectin adsorbed on the surface of zein appeared to form an elastic network structure, which increased the stability of stigmasterol nanodispersions. ZPNs not only relieved the adverse physiological symptoms of colitis in mice, but additionally prevented colonic length shortening and reduced fecal hemoglobin content. Immunohistochemical analysis showed that ZPNs could alleviate colitis by inhibiting the NF-κB signaling pathway involved in the expression of inflammatory factors TNF-α, IL-6, IL-1β, CSF-1 and coenzyme COX-2. This study suggests that supplement of nano-embedded stigmasterol based on zein and pectin has a positive therapeutic effect on alleviating colitis in mice. Such activities of nano-embedded stigmasterol in humans remain to be investigated.