Hypertensive retinopathy (HR) is a serious eye disease that can lead to permanent vision loss if not diagnosed early. The conventional diagnostic methods are subjective and time-consuming, so there is a need for an automated and reliable system. In this study, a three-stage method that provides high accuracy in HR diagnosis is proposed. In the first stage, 14 well-known Convolutional Neural Network (CNN) models were evaluated, and the top three models were identified. Among these models, DenseNet169 achieved the highest accuracy rate of 87.73%. In the second stage, the deep features obtained from these three models were combined and classified using machine learning (ML) algorithms including Support Vector Machine (SVM), Random Forest (RF), and Extreme Gradient Boosting (XGBoost). The SVM with a sigmoid kernel achieved the best performance (92% accuracy). In the third stage, feature selection was performed using metaheuristic optimization techniques including Genetic Algorithm (GA), Artificial Bee Colony (ABC), Particle Swarm Optimization (PSO), and Harris Hawk Optimization (HHO). The HHO algorithm increased the classification accuracy to 94.66%, enhancing the model’s generalization ability and reducing misclassifications. The proposed method provides superior accuracy in the diagnosis of HR at different severity levels compared to single-model CNN approaches. These results demonstrate that the integration of Deep Learning (DL), ML, and optimization techniques holds significant potential in automated HR diagnosis.