The application of deep learning algorithms for medical diagnosis in the real world faces challenges with transparency and interpretability. The labeling of large-scale samples leads to costly investment in developing deep learning algorithms. The application of human prior knowledge is an effective way to solve these problems. Previously, we developed a deep learning system for glaucoma diagnosis based on a large number of samples that had high sensitivity and specificity. However, it is a black box and the specific analytic methods cannot be elucidated. Here, we establish a hierarchical deep learning system based on a small number of samples that comprehensively simulates the diagnostic thinking of human experts. This system can extract the anatomical characteristics of the fundus images, including the optic disc, optic cup, and appearance of the retinal nerve fiber layer to realize automatic diagnosis of glaucoma. In addition, this system is transparent and interpretable, and the intermediate process of prediction can be visualized. Applying this system to three validation datasets of fundus images, we demonstrate performance comparable to that of human experts in diagnosing glaucoma. Moreover, it markedly improves the diagnostic accuracy of ophthalmologists. This system may expedite the screening and diagnosis of glaucoma, resulting in improved clinical outcomes. © 2021, The Author(s).