Corneal ulcer is a prevalent ocular condition that requires ophthalmologists to diagnose, assess, and monitor symptoms. During examination, ophthalmologists must identify the corneal ulcer area and evaluate its severity by manually comparing ocular staining images with severity indices. However, manual assessment is time-consuming and may provide inconsistent results. Variations can occur with repeated evaluations of the same images or with grading among different evaluators. To address this problem, we propose an automated corneal ulcer grading system for ocular staining images based on deep learning techniques and the Hough Circle Transform. The algorithm is structured into two components for cornea segmentation and corneal ulcer segmentation. Initially, we apply a deep learning method combined with the Hough Circle Transform to segment cornea areas. Subsequently, we develop the corneal ulcer segmentation model using deep learning methods. In this phase, the predicted cornea areas are utilized as masks for training the corneal ulcer segmentation models during the learning phase. Finally, this algorithm uses the results from these two components to determine two outputs: (1) the percentage of the ulcerated area on the cornea, and (2) the severity degree of the corneal ulcer based on the Type–Grade (TG) grading standard. These methodologies aim to enhance diagnostic efficiency across two key aspects: (1) ensuring consistency by delivering uniform and dependable results, and (2) enhancing robustness by effectively handling variations in eye size. In this research, our proposed method is evaluated using the SUSTech-SYSU public dataset, achieving an Intersection over Union of 89.23% for cornea segmentation and 82.94% for corneal ulcer segmentation, along with a Mean Absolute Error of 2.51% for determining the percentage of the ulcerated area on the cornea and an Accuracy of 86.15% for severity grading.