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Abstract Background Epidemiologic studies continue to emphasize that increasing patients with inflammatory bowel disease (IBD) develop to colorectal cancer (CRC). Although the function and mechanisms of IBD-associated genes (IBDGs) in CRC tumorigenesis have been extensively researched, the implications of IBDGs in the prognosis value and tumor immunity of CRC remain unclear. Results In this study, the expression, pathological stages and prognostic value of IBDGs in CRC were systematically analyzed, and 7 prognostic genes including CDH1, CCL11, HLA–DRA, NOS2, NAT2, TIMP1 and TP53 were screened through LASSO–Cox regression analysis. Then, a prognostic signature was established based on the 7 prognostic genes, and the model exhibited a good ability in risk stratification of CRC patients. Subsequent results showed that the genetic alterations of the 7 prognostic genes exhibited more significant and extensive influence on immune cells infiltration in colon adenocarcinoma than that in rectal adenocarcinoma. Meanwhile, immune cells infiltration also showed a significant difference between low-risk group and high-risk group. What’s more, 7 prognostic genes-based risk stratification was associated with microsatellite instability, and its prognostic characteristics were significantly negatively correlated with mismatch repair genes. Conclusions This study provided a promising insight that the 7 IBDGs could be used as valuable biomarkers for prognostic diagnosis and personalized immunotherapy of CRC patients.