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The global prevalence of ocular surface diseases (OSDs), such as dry eyes, conjunctivitis, and subconjunctival hemorrhage (SCH), is steadily increasing due to factors such as aging populations, environmental influences, and lifestyle changes. These diseases affect millions of individuals worldwide, emphasizing the importance of early diagnosis and continuous monitoring for effective treatment. Therefore, we present a deep learning-enhanced imaging system for the automated, objective, and reliable assessment of these three representative OSDs. Our comprehensive pipeline incorporates processing techniques derived from dual-mode infrared (IR) and visible (RGB) images. It employs a multi-stage deep learning model to enable accurate and consistent measurement of OSDs. This proposed method has achieved a 98.7% accuracy with an F1 score of 0.980 in class classification and a 96.2% accuracy with an F1 score of 0.956 in SCH region identification. Furthermore, our system aims to facilitate early diagnosis of meibomian gland dysfunction (MGD), a primary factor causing dry eyes, by quantitatively analyzing the meibomian gland (MG) area ratio and detecting gland morphological irregularities with an accuracy of 88.1% and an F1 score of 0.781. To enhance convenience and timely OSD management, we are integrating a portable IR camera for obtaining meibography during home inspections. Our system demonstrates notable improvements in expanding dual-mode image-based diagnosis for broader applicability, effectively enhancing patient care efficiency. With its automation, accuracy, and compact design, this system is well-suited for early detection and ongoing assessment of OSDs, contributing to improved eye healthcare in an accessible and comprehensible manner.