Background and Aim: Endoscopic evaluation of disease activity, including mucosal healing, is poorly established in Crohn's disease. We previously reported that patients with a Lewis score (LS) on capsule endoscopy < 270 had a lower risk of exacerbation without additional treatment. This study investigated prognostic predictors in patients undergoing capsule endoscopy and determined the optimal LS cut-off value. Methods: In a retrospective single-center study, 102 patients with Crohn's disease who underwent capsule endoscopy were reviewed. We reviewed the clinical course and the patients' characteristics, Crohn's Disease Activity Index, laboratory findings, LS, and Prognostic Nutritional Index (PNI) for factors potentially associated with Crohn's disease-related emergency hospitalization. Subsequently, we prospectively enrolled 66 patients with Crohn's disease and analyzed clinical outcomes according to these factors. Results: In the retrospective study, LS ≥ 270 and PNI < 45 were identified as independent predictors of Crohn's disease-related emergency hospitalization with hazard ratios of 9.48 and 3.01, respectively. Even in patients with LS ≥ 270, cumulative hospitalization rates decreased after intervention based on capsule endoscopy findings. The prospective study confirmed that patients with LS ≥ 270 or PNI < 45 had a significantly higher risk of Crohn's disease-related emergency hospitalization and that additional treatment reduced the risk of relapse. Conclusions: LS and PNI are the best available prognostic predictors in patients with Crohn's disease without gastrointestinal stenosis and can guide decisions on treatment escalation. Patients with LS ≥ 270 and PNI < 45 were at increased risk for exacerbation, and additional treatments should be considered for this group.