To investigate whether parameters from IDEAL-IQ/amide proton transfer MRI (APTWI) could help predict histopathological factors of rectal cancer. Preoperative IDEAL-IQ and APTWI sequences of 67 patients with rectal cancer were retrospectively analyzed. The intra-tumoral proton density fat fraction (PDFF), R2* and magnetization transfer ratio asymmetry (MTRasym (3.5 ppm)) were measured according to the histopathological factors of rectal cancer. The relationship between MR parameters and histopathological factors were analyzed, along with diagnostic performance of MR parameters. PDFF, R2* and MTRasym (3.5 ppm) were statistically different between T1+T2/T3+T4 stages, non-metastatic/metastatic lymph nodes, lower/higher tumor grade and negative/positive status of MRF and EMVI (p < 0.001 for PDFF, p = 0.000-0.015 for R2* and p = 0.000-0.006 for MTRasym (3.5 ppm)). There were positive correlations between the above parameters and the histopathological features of rectal cancer (r = 0.464-0.723 for PDFF (p < 0.001), 0.299-0.651 for R2* (p = 0.000-0.014), and 0.337-0.667 for MTRasym (3.5 ppm) (p = 0.000-0.005)). MTRasym (3.5 ppm) correlated moderately and mildly with PDFF (r = 0.563, p < 0.001) and R2* (r = 0.335, p = 0.006), respectively. PDFF provided a significantly higher diagnostic ability than MTRasym (3.5 ppm) for distinguishing metastatic from non-metastatic lymph nodes (z = 2.407, p = 0.0161). No significant differences were found in MR parameters for distinguishing other histopathological features (p > 0.05). IDEAL-IQ and APTWI were associated with histopathological factors of rectal cancer, and might serve as non-invasive biomarkers for characterizing rectal cancer.