In this study, we investigated the utility of native mapping in differentiating between various grades of fibrosis and compared its diagnostic accuracy to magnetization transfer imaging (MTI) in a rat model of CD. Bowel specimens (64) from 46 CD model rats undergoing native mapping and MTI were enrolled. The longitudinal relaxation time ( value) and normalized magnetization transfer ratio (MTR) were compared between none-to-mild and moderate-to-severe fibrotic bowel walls confirmed by pathological assessments. The results showed that the correlation between the value and fibrosis ( = 0.438, < 0.001) was lower than that between the normalized MTR and fibrosis ( = 0.623, < 0.001). Overall, the values ( = -3.066, = 0.004) and normalized MTRs ( = 0.081, < 0.001) in none-to-mild fibrotic bowel walls were lower than those in moderate-to-severe fibrotic bowel walls. The area under the curve (AUC) of the value (AUC = 0.716, = 0.004) was significantly lower than that of the normalized MTR (AUC = 0.881, < 0.001) in differentiating moderate-to-severe fibrosis from none-to-mild fibrosis ( = -2.037, = 0.042). Our results support the view that the value could be a promising imaging biomarker in grading the fibrosis severity of CD. However, the diagnostic performance of native mapping was not superior to MTI.