In the wake of population aging, prostate cancer has become one of the most important diseases in western elderly men. T2-weighted-images (T2WIs) provides the best depiction of the prostate’s anatomy, and diffusion‐weighted images (DWIs) provides clues of cancer as prostate cancer appears as an area of high signal on DWIs. However, high b-value DWIs is affected by the susceptibility effects. In this paper，we describe and utilize a fully automatic 3D deep neutral network to correct misalignment between T2WIs and DWIs. The average increasement of Dice coefficient of before-and-after registration is 73% and 84%, which reflects the removal of susceptibility effects.