With the continuous development of computer science and technology, the level of medical image processing and analysis technology has been significantly improved. In order to further optimize the medical imaging technology and provide assistance for medical diagnosis and treatment, this study will explore the head CT image segmentation technology and three dimensional reconstruction technology based on human anatomy, using two morphological operation methods of image expansion and image corrosion, as well as the triangulation method based on surface contour, Optimize CT image segmentation technology and three dimensional reconstruction technology. The results show that the CT image segmentation technology based on human anatomy can obtain the more essential morphology and features of the target image, and significantly improve the image quality. The size of the threshold can have a certain impact on the 3D reconstruction effect and reconstruction time to a certain extent. The larger the threshold, the shorter the reconstruction time, but the worse the 3D reconstruction effect. This shows that the target image after fitting has a good reconstruction effect, but the threshold level should be kept at a low level. The head CT image segmentation technology and three dimensional reconstruction technology based on human anatomy have good application effects and can be popularized and applied in clinical diagnosis and treatment.