Abstract Background Colorectal cancer (CRC) is related to gut microbiota dysbiosis, especially butyrate-producing bacteria reduction. Our previous study suggested administration of Clostridium butyricum (C. butyricum), a butyrate-producing bacterium, exerts a crucial effect against CRC. Methyltransferase-like 3 (METTL3) contributes to tumorigenic epigenetic regulation. We aimed to investigate the effects of C. butyricum on METTL3 in the prevention of CRC. Methods TCGA and CancerSEA databases were used to investigate METTL3 co-expressed genes, and the GO and KEGG enrichment analysis was conducted on METTL3. Tissue specimens of human normal colonic tissue, adenoma and carcinoma were obtained and examined the expression of METTL3, EMT-associated markers, and VM formation. We overexpressed METTL3 in CRC cells to assess cell migration and tube formation. Meanwhile, the effects of C. butyricum on METTL3, epithelial-mesenchymal transition (EMT), and vasculogenic mimicry (VM) formation in CRC cells were evaluated. Furthermore, a murine xenograft model was established to provide further evidence of the inhibition of C. butyricum on tumor growth. Results Database analysis suggested that METTL3 showed a positive correlation with proliferation, EMT, DNA repair, metastasis, and invasion. The expression of METTL3 gradually increased from human normal colon tissue, adenoma to carcinoma, and was positively correlated with VM formation and EMT. METTL3 overexpression promoted the proliferation, migration, and invasion of CRC cells and induced VM formation. C. butyricum could downregulate METTL3 expression in CRC cells and decrease the expression of vimentin and vascular endothelial growth factor receptor 2 to reduce EMT and VM formation. Moreover, C. butyricum alleviated the pro-oncogenic effect of METTL3 overexpressing plasmid in CRC cells. Accordingly, C. butyricum downregulated the expression of METTL3 in tumors and prevented EMT in nude mice. Conclusion C. butyricum could inhibit EMT and VM of intestinal carcinogenesis through downregulating METTL3. These findings broaden our understanding of probiotics supplement in the prevention and treatment of CRC.