AIM: To investigate the relationship between anaemia and bone marrow fat fraction (BMFF) based on chemical shift-encoded magnetic resonance imaging (CSE-MRI) in Crohn's disease (CD) patients. MATERIALS AND METHODS: A total of 103 patients with CD and 67 healthy volunteers were enrolled in this study. Differences in BMFF, red blood cell (RBC), and haemoglobin (Hb) counts were compared between the two groups. The correlation between indicators of anaemia and BMFF, the relationship between changes in BMFF and the odds ratio of anaemia, and its linear dose-response association were evaluated. Finally, the areas under the receiver operating characteristic curves (AUCs) for BMFF in predicting anaemia were calculated. RESULTS: BMFF, RBC, and Hb levels were significantly lower in the CD group than in the control group (all P </= 0.05). After adjusting for age, sex, and body mass index (BMI), there was a moderate positive correlation between BMFF and Hb in patients with CD (r = 0.445, P < 0.001). No significant correlation was present between BMFF and RBC (r = 0.183, P = 0.069). The change in BMFF was negatively associated with the odds ratio of anaemia even after adjustment for demographic and CD characteristics (all P </= 0.001). Restricted cubic spline (RCS) regression showed a linear dose-response association between BMFF and the odds ratio of anaemia (P overall = 0.004, P for nonlinearity = 0.652). The AUC to differentiate between anaemia and nonanaemia was 0.703 for BMFF. CONCLUSION: Decreased BMFF is associated with a high risk of anaemia in patients with CD.