Abstract Objectives To integrate multiple parameters derived from unenhanced spectral CT with 3D-printing technique to accurately evaluate intestinal lesions in patients with Crohn’s disease (CD). Methods Patients with proven CD who underwent preoperative spectral CT and surgery were included. The spectral CT images and histopathological specimens were achieved by employing 3D-printing technique. Diagnostic models were developed utilizing Z-Effective, Electron Density (ED), and Hounsfield unit (HU) values derived from spectral CT, along with spectral curve slopes λ1 and λ2, as well as ΔHUMonoE. The area under the receiver operating characteristic curve (AUC) and the influence of inflammation on the efficacy of the models were analyzed. Results The ED and HU at MonoE 50 keV of the spectral CT were determined to exhibit the highest correlation with the fibrosis degree of the diseased intestine. The training dataset yielded an AUC of 0.828 (95% CI: 0.705–0.951). The sensitivity and specificity were calculated to be 77.3% and 82.6%, respectively. The AUC of the validation set was 0.812 (95% CI: 0.676–0.948) with a sensitivity of 63.6% and specificity of 89.7%. Moreover, our model demonstrated enhanced diagnostic accuracy for detecting fibrosis with an AUC value of 0.933 (95% CI: 0.856–1.000), sensitivity of 90.9%, and specificity of 87.0%, after regulating the influence of inflammation. Conclusion The integration of unenhanced multi-parametric spectral CT and 3D-printing technique seems to be able to assess the intestinal fibrosis. Our diagnostic model remains effective in assessing the severity of fibrosis under presence of inflammation. Critical relevance statement Our diagnostic model accurately assessed the degree of intestinal wall fibrosis in Crohn’s disease patients by using unenhanced spectral CT and 3D-printing technique, which could facilitate individualized treatment. Key Points Evaluating the extent of Crohn’s disease-related fibrosis is important. The combination of 3D-printing technique and multi-parametric spectral CT enhances diagnostic accuracy. The developed model using spectral CT allows for the assessment of intestinal fibrosis using multi-parameters. Graphical Abstract