The invention discloses a heart three-dimensional positioning method based on MR horizontal axis image segmentation, which comprises the following steps: scanning multiple layers of MR horizontal axis images, segmenting a heart region by using a region growing segmentation algorithm, reconstructing a three-dimensional heart image, manually adjusting a positioning surface, calculating parameters of a scanning surface, and inputting the parameters into a scanning instrument to complete scanning of four-cavity heart, horizontal axis and long axis of the heart. Compared with a manual positioning method, the method has the advantages that scanning surfaces such as a long axis, a short axis and a four-cavity heart of the heart can be directly scanned only by scanning a thoracic cavity image at a horizontal axis position, obtaining scanning surface parameters through post-processing and inputting the scanning surface parameters into a magnetic resonance scanning system, so that the time consumed by a positioning process is shortened, and the accuracy of heart positioning is improved.