Objective To evaluate the changes in magnetic resonance imaging-based body composition parameters during follow-ups in patients with Crohn's disease (CD). Methods Between November 1, 2017, and June 30, 2021, patients diagnosed with CD, who underwent two or more magnetic resonance enterography (MRE) scans at our institution were retrospectively reviewed. The baseline and one subsequent follow-up scan for each patient were paired to form longitudinal comparisons. Skeletal muscle, visceral adipose tissue (VAT), and subcutaneous adipose tissue (SAT) indexes were calculated from tissue areas measured at the third lumbar vertebra level per scan, standardized by dividing the height(2) and lumbar height(2) (height(L1-L5)). We also assessed the correlation between changes in VAT to total adipose tissue ratio (VA/TA index) and CD activity scores (5-point MRE classification) using Spearman's correlation analysis. A multivariate linear regression model was used to adjust for the follow-up duration and treatment type. Results Overall, 49 patients (with 49 paired scans) were enrolled. VA/TA index changes were negatively correlated with changes in skeletal muscle index (SMI; r = - 0.339, p < 0.05). The VA/TA index (52.69 +/- 10.66% vs. 49.18 +/- 10.80%, p < 0.001) and the total MRE score (8.0 +/- 3.9 vs. 5.7 +/- 3.4, p < 0.001) decreased significantly during follow-up, regardless of follow-up duration and treatment type (both p > 0.05). Changes in total MRE score were negatively correlated with SMI changes (r = - 0.408, p < 0.01) but positively correlated with VA/TA index changes (r = 0.479, p < 0.01). Conclusion An increase in SMI and a decrease in VA/TA index could reflect improved nutritional and inflammatory status.