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Corneal endothelial dysfunction is a major cause of global blindness, with an estimated 12.7 million patients awaiting corneal transplantation, and the severe shortage of donor grafts underscores the urgent need for non-surgical therapies. Gene therapy offers a promising alternative, but is hindered by the limitations in existing delivery systems and the scarcity of validated molecular targets capable of reversing core pathophysiology. To address this, we first employed multi-omics analysis and identified FOXO1 as a central and under-explored therapeutic target for corneal endothelial dysfunction. In vivo FOXO1 overexpression effectively improved corneal endothelial function by preserving mitochondria-associated endoplasmic reticulum membrane integrity and mitochondrial Ca^{2 +} homeostasis, yet its therapeutic potential was limited by low transfection efficiency. To overcome this, we engineered an AAV-Foxo1 delivery system using a viscous choline chloride-fructose-based deep eutectic solvent (DES) as the carrier. The DES-AAV-Foxo1 delivery system exhibited good biocompatibility, significantly prolonged anterior chamber retention, and enhanced transfection efficiency in corneal endothelial cells compared to conventional AAV delivery. Animal experiments confirmed that it effectively improved corneal endothelial pump activity and mitigates endothelial dysfunction in type 1 diabetes mellitus and Fuchs endothelial corneal dystrophy mouse models. Our findings demonstrated the therapeutic potential of DES-AAV-Foxo1 delivery system for corneal endothelial disorders.