The invention discloses a brain MR medical image registration method. The method comprises the steps of 1, segmenting a reference image and a floating image by adopting a BCFCM method; 2, performing symmetry axis detection on the original reference image and the original floating image by adopting an MSR detection method, and extracting a symmetry axis equation; 3, performing threshold segmentation on the image processed in the step 1; 4, performing approximate symmetry constraint on the image processed in the step 3 according to the symmetry axis equation detected in the step 2, and marking the obtained image as a reference image and a floating image to be registered; 5, initializing rigid body transformation matrix registration parameters; and 6, registering the image through an SSD similarity measurement criterion to obtain an optimal transformation matrix registration parameter, segmenting the reference image and the floating image by using a BCFCM method; and performing binarization threshold processing on the segmented image to separate the background before separation, performing symmetry constraint on the image after binarization processing, and applying the image after binarization processing to multi-modal image registration under an SSD framework. The registration efficiency, the precision and the robustness are improved.