Disclosed are a method and apparatus for registering images having different modalities. The medical image registration method includes performing, at an initial register, multi-modality registration of a reference image from a plurality of first images captured during a first breathing period and a second image; performing, at the initial register, single-modality registration of the reference image and each of the other first images; generating registration images between the plurality of first images and the second image based on the multi-modality registration and the single-modality registration; acquiring a third image captured after the first breathing period; and detecting an image corresponding to the third image from the registration images.