To explore the sub-regional histogram features of amide proton transfer-weighted (APTw) MRI, compared with those of diffusion-weighted imaging (DWI), in predicting the tumor budding (TB) grade of rectal cancer (RC). This study prospectively enrolled 74 patients with pathologically confirmed RC, who underwent APTw MRI before surgery from July 2022 to March 2023. Hematoxylin-eosin staining was used for TB scoring. K-means clustering (K = 4-6) was applied to obtain multiple sub-regions (n = 3-5), and corresponding histogram features (including mean, standard deviation, minimum, maximum, and 10th, 25th, 50th, 75th, and 90th quantile) of APT and apparent diffusion coefficient (ADC) maps were extracted and filtered using stepwise regression. When K = 5, the K-means clustering is four sub-regions, showing the best prediction for TB grade compared to K = 4 or 6. When K = 5, there were significantly higher histogram features of the APT map in sub-regions 3 and 4 in the high TB grade group compared to the low-intermediate TB grade group. Receiver operating characteristic (ROC) curve and internal validation suggested that the predictive efficiency of the model was highest when K = 5, with AUC, sensitivity, specificity, accuracy, and kappa values of 0.92, 93%, 71%, 87%, and 0.65, respectively. There were no significant differences in the histogram features of each sub-region in the ADC map (p > 0.05). The sub-regional histogram features of APTw images can help to distinguish the heterogeneous regions of RC, which can be used to predict the TB grade of RC. Question Can the sub-regional histogram features of APTw MRI predict the tumor budding (TB) grade of rectal cancer (RC)? Findings Differences exist in histogram features of APT map subregions between high and low-intermediate TB grade groups; subregions of the APT map have different predictive abilities. Clinical relevance APT-weighted imaging might outperform DWI in predicting TB grade in RC.