The present invention discloses a method and a system of vertebral compression fracture detection. The method of vertebral compression fracture detection includes: recombining a plurality of anatomical images captured in at least a spine segment of a target individual into a 3D image; using a multi-planar reconstruction method to reformat the 3D image to obtain at least one sagittal reformatted image; using a classification model to determine whether the sagittal reformatted image covers the middle section of the vertebral column or not; using a vertebral detection method to detect each vertebral body in the sagittal reformatted image covering the middle section of the vertebral column; using a keypoint localization method to localize a plurality of keypoints of each vertebral body which was detected in the sagittal reformatted image; evaluating the compression fracture grade of each vertebral body in the sagittal reformatted image.