The invention discloses a multi-elite immune quantum clustering-based medical image segmenting system and a multi-elite immune quantum clustering-based medical image segmenting method, which relate to the technical field of image processing. The system comprises a preprocessing module, a data preparing module, a data clustering module and a segmentation result output module. The process for segmenting a medical image by the modules comprises the following steps: 1) preprocessing the medical image to be segmented; 2) coding antibodies and initializing an antibody population; 3) calculating antibody affinity, and dividing the antibody population into an elite population and a general population; 4) designing different multi-elite immune optimization operators for the elite population and the general population respectively, and performing a cloning operation, a cloud mutation operation, an all-interference recombination operation, a selecting operation and a hypercube interlace operation orderly; and 5) outputting a medical image segmentation result. The multi-elite immune quantum clustering-based medical image segmenting system and the multi-elite immune quantum clustering-based medical image segmenting method can effectively segment the medical image which contains large-scale data volume, has an accurate and precise segmentation result, and can be used for auxiliary diagnosis of the medical image and pathogenesis research.