Abstract: During the facture of image cell, on the reason of the equipment and something man-made, there will be things that the overlapping degree of overlapping cell distributes asymmetrically, which will infect the result of the segmentation, so it will bring difficulty to the following statistic and analysis. This article advance a new processing method, which combine watershed algorithm and self-adapt distance transform. In this method, we add the information of the degree of overlapping to the function of distance transform. Therefore, the function of distance transform can change its parameter along with the change of the degree of the overlapping consequently, thus the over separating and the lack of separating can be avoid effectively. Experiment proved that the new method can separate the overlapping cell images successfully and steadily.