The present disclosure provides an operating method of a brain imaging neurological abnormality prediction system, which includes steps as follows. The T1-weighted image and the diffusion-weighted image of the patient are acquired; the image process is performed on the T1-weighted image and the diffusion-weighted image to obtain a smoothed brain standard space infarction image; the smoothed brain standard space infarction image is multiplied by and a weighted image for a post-processing to obtain a post-weight image; the post-weight image is inputted to the deep learning cross validation classification model of transfer learning to predict whether the neurological abnormality occurs within a predetermined period after the patient's brain disease.