The invention discloses a cell nucleus segmentation method and system of fluorescence in situ hybridization images. The method realizes the recognition and segmentation of cell nucleus in FISH imagesthrough pretreatment, binarization, hole filling, morphological operation, secondary watershed and other processing processes. The system comprises a FISH image receiving module, an image preprocessing module, a cell nucleus detecting module and a report generating module. When the FISH images of breast cancer, gastric cancer and other cancer cells are segmented to obtain the cell nucleus region,the invention can reduce the image fluorescence scattering effect through multiple pretreatments, can effectively improve the over-segmentation problem easily caused by the direct watershed, and thusimprove the segmentation quality of the FISH image recognition cell.