Introduction: Obesity is associated with an increased risk of inflammatory bowel disease (IBD), whereas not all obesity individuals have the same effect. In individuals with obesity, the role of metabolic status in the readmission of IBD remains unclear. Our study aimed to evaluate the association between different obesity metabolic phenotypes and the prognosis of IBD patients. Methods: We conducted a longitudinal cohort study using Nationwide Readmission Database (2018 sample). Out of 12,928,231 discharge records, 63,748 records with a discharge diagnosis of IBD were identified for analysis. Cox proportional hazard ratio (HR) with 95% confidence interval (CI) was calculated adjusting for potential confounders. Results: During 180-day follow-up in IBD patients with different obesity metabolic phenotypes, all-cause readmission rate, inpatient mortality rate, unplanned readmission rate, total charge, hospitalized length of stay were statistical different (all P<0.001). After multivariate Cox regression analysis, IBD patients with metabolically unhealthy nonobese (MUNO) had higher risk of readmission (all-cause and unplanned) (HR 1.04, 95% CI 1.00-1.08 and HR 1.06, 95% CI 1.02-1.10), and that with metabolically unhealthy obesity (MUO) had higher risk of unplanned readmission (HR 1.08, 95% CI 1.02-1.15). In subgroup analysis, both MUNO group and MUO group had higher risk of readmission (all-cause and unplanned) in UC subgroup; but only MUNO group had higher risk of readmission (all-cause and unplanned) (HR 1.05, 95% CI 1.00-1.10 and HR 1.06, 95%CI 1.01-1.12) in CD subgroup. Conclusion: Metabolic abnormalities were associated with an increased risk of readmission in patients with IBD, regardless of obesity.