Crohn's disease (CD) and intestinal tuberculosis (ITB) share similar histopathological characteristics, and differential diagnosis can be a dilemma for pathologists. This study aimed to apply deep learning (DL) to analyze whole slide images (WSI) of surgical resection specimens to distinguish CD from ITB. Overall, 1973 WSI from 85 cases from 3 centers were obtained. The DL model was established in internal training and validated in external test cohort, evaluated by area under receiver operator characteristic curve (AUC). Diagnostic results of pathologists were compared with those of the DL model using DeLong's test. DL model had case level AUC of 0.886, 0.893 and slide level AUC of 0.954, 0.827 in training and test cohorts. Attention maps highlighted discriminative areas and top 10 features were extracted from CD and ITB. DL model's diagnostic efficiency (AUC = 0.886) was better than junior pathologists (*1 AUC = 0.701, P = 0.088; *2 AUC = 0.861, P = 0.788) and inferior to senior GI pathologists (*3 AUC = 0.910, P = 0.800; *4 AUC = 0.946, P = 0.507) in training cohort. In the test cohort, model (AUC = 0.893) outperformed senior non-GI pathologists (*5 AUC = 0.782, P = 0.327; *6 AUC = 0.821, P = 0.516). We developed a DL model for the classification of CD and ITB, improving pathological diagnosis accuracy effectively.