This study explored the application of APT and IVIM in evaluation of prognostic factors for rectal adenocarcinoma. Parameters of APT signal intensity (APT SI), pure diffusion coefficient (D), pseudo-diffusion coefficient (D*), perfusion fraction (f), and apparent diffusion coefficient (ADC) were measured. The results showed that APT SI was significantly lower in low- than high-grade adenocarcinoma. The D value was significantly higher in low- than high-grade adenocarcinoma. The D value was significant lower in positive than in negative extramural vascular invasion (EMVI). This suggests that APT and IVIM were helpful to assess rectal adenocarcinoma, including histopathological grade and the EMVI status.