Compared with the previous automatic segmentation neural network for the target area which considered the target area as an independent area, a stacked neural network which uses the position and shape information of the organs around the target area to regulate the shape and position of the target area through the superposition of multiple networks and fusion of spatial position information to improve the segmentation accuracy on medical images was proposed in this paper. Taking the Graves’ ophthalmopathy disease as an example, the left and right radiotherapy target areas were segmented by the stacked neural network based on the fully convolutional neural network. The volume Dice similarity coefficient (DSC) and bidirectional Hausdorff distance (HD) were calculated based on the target area manually drawn by the doctor. Compared with the full convolutional neural network, the stacked neural network segmentation results can increase the volume DSC on the left and right sides by 1.7% and 3.4% respectively, while the two-way HD on the left and right sides decrease by 0.6. The results show that the stacked neural network improves the degree of coincidence between the automatic segmentation result and the doctor's delineation of the target area, while reducing the segmentation error of small areas. The stacked neural network can effectively improve the accuracy of the automatic delineation of the radiotherapy target area of Graves' ophthalmopathy.