Objective The precise segmentation of organs at risk (OARs) is of importance for improving therapeutic outcomes and reducing injuries of patients undergoing radiotherapy. In this study, we developed a new approach for accurate computed tomography (CT) image segmentation of the eyes and surrounding organs, which is first locating then segmentation (FLTS). Methods The FLTS approach was composed of two steps: (a) classification of CT images using convolutional neural networks (CNN), and (b) segmentation of the eyes and surrounding organs using modified U-shape networks. In order to obtain optimal performance, we enhanced our training datasets by random jitter and rotation. Results This model was trained and verified using the clinical datasets that were delineated by experienced physicians. The dice similarity coefficient (DSC) was employed to evaluate the performance of our segmentation method. The average DSCs for the segmentation of the pituitary, left eye, right eye, left eye lens, right eye lens, left optic nerve, and right optic nerve were 90%, 94%, 93.5%, 84.5%, 84.3%, 80.3%, and 82.2%, respectively. Conclusion We developed a new network-based approach for rapid and accurate CT image segmentation of the eyes and surrounding organs. This method is accurate and efficient, and is suitable for clinical use.