Background This study aimed to 1) assess the independent factors affecting patients with postoperative intestinal fistula from Crohn’s disease by analyzing preoperative clinical data, 2) establish a nomogram prediction model for this condition based on these factors, and 3) validate this model and evaluate its accuracy.Methods In this retrospective multicenter case-control study, the clinical data of 240 patients with Crohn’s disease admitted for surgical treatment between September 2017 and September 2019 at three centers were collected. Patients were randomly divided into a training set (168 patients) and a validation set (72 patients). Univariate analysis was performed for relevant factors, and statistically significant factors were then analyzed by multivariate logistic regression to determine the independent influencing factors. A nomogram model for predicting postoperative intestinal fistula in patients with Crohn’s disease was constructed and its accuracy of the model evaluated using calibration curves.Results Univariate analysis showed that disease behavior, abdominal abscess, intestinal perforation, neutrophil-to-lymphocyte ratio, systemic immunoinflammatory index, and prognostic nutrition index were factors affecting postoperative intestinal fistula in patients with Crohn’s disease. Multivariate logistic regression analysis showed that neutrophil-to-lymphocyte ratio, prognostic nutrition index, disease behavior, and Crohn's disease activity index score were independent influencing factors. After assessing the validation set, the area under the curve was 0.899, indicating good predictive accuracy of the nomogram model.Conclusions The prediction model developed in this study can effectively predict the risk of postoperative intestinal fistula.