The invention discloses a multi-modality medical image processing method based on multilevel threshold segmentation. The method comprises the following steps: 1, corresponding medical image gray scale image data are acquired; 2, a Gauss scale space model is built to complete denoising processing at the same time; 3, anisotropic nonlinear diffusion and 0-paradigm gradient minimization model are adopted to complete smoothing processing on the medical image; 4, a search algorithm range for the best threshold in an OTSU image segmentation algorithm is narrowed, and the search algorithm efficiency is improved; and 5, through effectively using the space position information, a complete segmentation area is extracted to obtain better segmentation effects. At an image pre-processing denoising stage, a multi-scale Gauss model is built, and denoising effects are better compared with a single-scale model; at a stage of adopting the multi-threshold OTSU segmentation method, the algorithm threshold search range is narrowed, and the segmentation algorithm operation efficiency is improved; and thus, the method of the invention has the advantages of good real-time performance and accurate segmentation effects.