Provided is a multi-modality medical image analysis method and apparatus for brain disease diagnosis. The method includes the steps of: acquiring medical images with different modalities for the same patient; selecting at least some of pre-trained analysis models corresponding to the modalities of the medical images; inputting the medical images correspondingly to the analysis models selected with respect to the modalities of the medical image to produce output values related to a plurality of factors used for reading at least one brain disease; converting the output values to produce a plurality of feature vectors corresponding to the output values; and inputting the plurality of feature vectors to at least one diagnosis model pre-trained to read the brain disease to thus predict a degree of brain disease progression.