Objectives To investigate the utility of 3D amide proton transfer (APT) MRI in predicting pathologic factors for rectal adenocarcinoma, in comparison with diffusion kurtosis imaging. Methods Sixty-one patients with rectal adenocarcinoma were enrolled in this prospective study. 3D APT and diffusion kurtosis imaging (DKI) were performed. Mean APT-weighted signal intensity (APTw SI), mean kurtosis (MK), mean diffusivity (MD), and ADC values of tumors were calculated on these maps. Pathological analysis included WHO grades, pT stages, pN stages, and extramural venous invasion (EMVI) status. Student's t test, Spearman correlation, and receiver operating characteristics (ROC) analysis were used for statistical analysis. Results High-grade rectal adenocarcinoma showed significantly higher mean APTw SI and MK values (2.771 +/- 0.384 vs 2.108 +/- 0.409, 1.167 +/- 0.216 vs 1.045 +/- 0.175, respectively; p < 0.05). T3 rectal adenocarcinoma demonstrated higher mean APTw SI and MK than T2 tumors (2.433 +/- 0.467 vs 1.900 +/- 0.302, p < 0.05). No kurtosis, diffusivity, and ADC differences were found between T2 and T3 tumors. Tumors with lymph node metastasis and EMVI involvement showed significantly higher mean APTw SI, MK. No difference was found in diffusivity and ADC between pN0 and pN1-2 groups, and EMVI-negative and EMVI-positive statuses. Mean APTw SI exhibited a significantly high positive correlation with WHO grades, demonstrating 92.31% sensitivity and 79.17% specificity for distinguishing low- from high-grade rectal adenocarcinoma, providing a better diagnostic capacity than MK, MD, and mean ADC values. Conclusion 3D-APT could serve as a non-invasive biomarker for evaluating prognostic factors of rectal adenocarcinoma.