A retrospective study in a tertiary care hospital included 376 hospitalized patients with Crohn's disease (CD) between 2015 and 2025. Thirty-six patients (9.6%) had metabolic syndrome (MetS). Patients with MetS had significantly higher simple endoscopic scores for CD (10 vs. 7; p < 0.001) and Crohn's disease activity index (294.3 vs. 256.6; p < 0.001) than patients without MetS. They had a higher risk of complications (OR = 8.65, 95% CI: 2.1–?, p = 0.004) and surgical or invasive procedures (OR = 2.64, 95% CI: 1.27–5.45, p = 0.009). Low levels of high-density lipoprotein cholesterol increased the risk of adverse outcomes. The cumulative number of MetS components had an incremental effect, where increasing number of components was associated with higher disease severity and risk of poor outcomes. The simultaneous presence of multiple elements of MetS may synergistically worsen the clinical course of CD. Management of these components is critical to the long-term prognosis of CD.