The present invention relates to a method for segmenting overlapping cytoplasm in a medical image, including: establishing a cytoplasm shape hypothesis set (201); and selecting a shape hypothesis for each cytoplasm from the established cytoplasm shape hypothesis set to perform constrained multi-shape evolution (202), thereby segmenting overlapping cytoplasm in the medical image, wherein the constrained multi-shape evolution (202) includes: segmenting a clump area composed of a plurality of overlapping cytoplasm to provide clump evidence (301); performing shape alignment to assess quality of the selected shape hypotheses (302); and performing shape evolution to determine a better shape hypothesis for each cytoplasm (3). The present invention further relates to a system for segmenting overlapping cytoplasm in a medical image. The method and system of the present invention can perform shape prior-based overlapping cytoplasm segmentation more accurately and more effectively.