Mesenchymal stem cell (MSC)-derived exosomes have the potential to sustain immune homeostasis and facilitate tissue regeneration, and those effects can be potentiated under three-dimensional (3D) cell culture conditions. Nevertheless, whether exosomes derived from 3D-cultured MSCs (3D-Exos) exert therapeutic effects on the injured corneas and the underlying mechanism remain unclear. In this study, MSCs are cultured in a gelatin methacryloyl (GelMA) hydrogel to produce 3D-Exos. In vitro experiments revealed that the 3D-cultured MSCs maintained their stemness, the exosomes were produced in better yield, and the generated 3D-Exos possess exceptional anti-inflammatory, pro-proliferative and tissue remodeling properties. Moreover, the 3D-Exos that were delivered by the GelMA hydrogel displayed a sustained release profile for multi-dimensional injured cornea repair. Extensive in vitro studies further demonstrated that, compared with the two-dimensional (2D)-Exo-hydrogel treatment, 3D-Exo-hydrogel treatment yielded better recovery of corneal morphology and function, as revealed by mitigated inflammation, promoted corneal epithelium and limbus repair, and reduced scar formation in the stroma. Mechanistically, the 3D-Exos promoted the proliferation of cornea-derived cells and reduced the release of inflammatory factors via miR-150-5p targeting of the PDCD4 gene. Overall, the developed 3D-Exo-hydrogel sustained release system may represent a promising cell-free strategy for the treatment of various corneal diseases.