BackgroundResidual abnormalities on computed tomography enterography (CTE) in Crohn's disease (CD) with endoscopic healing (EH) may have prognostic implications and affect therapeutic strategy. MethodsCD patients with EH who underwent CTE between March 2015 and June 2022 were enrolled. CTE findings of the terminal ileum and the most severe segment of colon at the time of EH were assessed respectively for each patient. Cox regression analysis and Kaplan-Meier curves were used to evaluate the association between residual abnormalities and adverse outcomes. ResultsA total of 140 patients (217 digestive segments) were included. Mesenteric edema (hazard ratio [HR] = 3.61, 95% CI = 1.81–7.20, P<0.001), fibrofatty proliferation (HR = 3.40, 95% CI = 1.97–5.85, P<0.001) and active small bowel inflammation (HR = 2.74, 95% CI = 1.59–4.71, P<0.001) were risk factors for clinical relapse. Furthermore, we built a scoring system using the three parameters. Radiologic score ≥ 1 was the best threshold to predict clinical relapse (HR = 4.56, 95% CI = 2.54–8.19, P<0.001) and it was validated in different outcomes. ConclusionThe scoring system based on three residual abnormalities on CTE can predict adverse outcomes in CD patients with EH.