These results suggest that Wnt3a and Fzd3 may not work together in activating canonical Wnt signaling to accelerate intestinal stem cell proliferation by promoting the transcription of c-myc and cyclin D. After MSCT, canonical Wnt signaling-related genes such as Wnt3a, Fzd3, β-catenin, TCF4, and cyclin D exhibited downregulation, and GSK-3β exhibited upregulation, compared with IBD rats; the canonical Wnt signaling pathway may be inhibited when treated with MSCs. This evidence concerns the gene TCF4 and inflammatory bowel disease.