Diffusion-weighted imaging (DWI) during MR enterography helps identify bowel inflammation in Crohn's disease (CD). However, image quality is compromised by geometric distortions from B0 field variations and physiological motion, making it challenging for radiologists to correlate findings between DWI and structural images. Traditional correction methods using reversed polarity scans are ineffective due to motion between acquisitions, which limits accurate estimation of intravoxel incoherent motion (IVIM) parameters. We propose a dual-echo echo-planar imaging (EPI) method that retrospectively corrects both geometric distortions and motion in 3T bowel DWI by accounting for field changes during peristalsis and breathing. We added a 5- to 7-min dual-echo EPI DW sequence (eight b-values, six directions) to the clinical MR enterography protocol of 21 patients with suspected CD at 3T MRI. Distortion correction was applied based on dynamically estimated fields from dual-echo DWI, followed by intra-volume registration between odd-even slices and inter-volume registration for motion correction. Two experienced board-certified radiologists evaluated the severity of the disease using simplified magnetic resonance index of activity (MaRIA) scores. Based on their consensus scores, patients were categorized into three groups: no active disease (MaRIA score = 0), active disease (MaRIA score = 1-2), and severe disease (MaRIA score = 3-5). The proposed DWI correction pipeline improved DWI/T2-weighted image Dice similarity from 0.73 to 0.89, enabling better correlation of findings between structural and DW-MR images and enhancing DWI's clinical value. Corrected IVIM parameters showed stronger correlations with MaRIA scores (D: ρ = -0.93; f: ρ = -0.94, p < 0.001) compared to uncorrected parameters (D: ρ = -0.68, p = 0.001; f: ρ = -0.35, p = 0.118). Diagnostic sensitivity increased from 0.44 to 0.89, while parameter uncertainty decreased from 35.58% to 19.31% for D and 63.48% to 40.40% for f (p < 0.001). These improvements strengthen quantitative IVIM imaging for CD assessment, potentially reducing reliance on contrast imaging while offering enhanced tissue perfusion and diffusion insights.