The invention relates to a deformation medical image registration method based on PCA and diffeomorphism Demons, and belongs to the technical field of medical image processing. According to the method, preprocessing is carried out on collected images, a multiresolution mechanism is then adopted, registration circulation is carried out under set iterations, a deformation field of movable images is calculated, smoothing is carried out through a Gaussian filter, interpolation is carried out on the movable images in an index domain by utilizing an obtained deformation field matrix, key features of the images are extracted by using PCA, and similarity measure between two images is calculated by combining SSD, Pearson, Spearman and Kendall. Compared with a traditional demons method, a PCA diffeomorphism log demons related registration method reduces calculated quantity, can restrain noise quite well, and is higher in robustness than a method that SSD similarity measure is merely adopted, the convergence speed is increased.