Abstract: Objective: The medical image segmentation is the foundation of the follow-up operation,just like 3D reconstruction,...etc.of CT Image.Accuracy of Segmentation is very important to the doctor’s judging.This paper study thoroughly the threshold value segmentation arithmetic and deve-lop a kind of software to solve the medical image multi-threshold value segmentation. Method: This software adopts Visual C++ program tools to carry on a development.It’s function module is mak-ing use of the importation document of the MITK to withdraw and deal with the importation data by the pixel value. Conclusion: Compared with the single threshold value segmentation,Multi-thre-shold value segmentation has many advantages.