The invention relates to a multimodal carotid MRI registration method based on physical alignment and contour matching. The method comprises steps that 1), image space physical coordinates are calculated; 2), body pixel spacing conversion image formats are unified; 3), the alignment relationship of multi-modal image layers is determined; 4), inner wall segmentation of multi-modal 2D images of eachsequence is carried out, a sequence of MRI images is sequentially selected, segmentation start and termination layers of the sequence images are determined, the ROI where a carotid is located in thestart layer image is selected, and the segmentation method is utilized to realize continuous automatic segmentation of the entire sequence; and 5), 3D registration based on the inner wall contour is carried out, and the clear inner wall contour segmentation result is utilized to carry out three-dimensional continuous registration. The method is advantaged in that carotid multimodal sequence imagesin various types are effective, alignment registration among pixels is excellently realized, and doctors are facilitated to carry out subsequent diagnosis and treatment determination and patch composition analysis.