Cholangiocarcinoma (CCA) has high recurrence rates that severely limit long-term survival. Effective tools for accurate recurrence monitoring and diagnosis remain lacking. Metabolic reprogramming, a key driver of CCA growth and recurrence, is underutilized in cancer screening and management. This study aimed to identify metabolite-based biomarkers to evaluate recurrence severity, enhance disease management, and elucidate the molecular mechanisms underlying CCA recurrence.