Probabilistic atlas based on human anatomical structure has been widely used for organ segmentation. The challenge is how to register the probabilistic atlas to the patient volume. Additionally, there is the disadvantage that the conventional probabilistic atlas may cause a bias toward the specific patient study due to a single reference. Hence, we propose a template matching framework based on an iterative probabilistic atlas for organ segmentation. Firstly, we find a bounding box for the organ based on human anatomical localization. Then, the probabilistic atlas is used as a template to find the organ in this bounding box by using template matching technology. Comparing our method with conventional and recently developed atlas-based methods, our results show an improvement in the segmentation accuracy for multiple organs (p < 0:00001).