Ectatic corneal diseases are a group of eye disorders characterized by progressive thinning and outward bulging of the cornea, resulting in vision impairment. A few attempts have been made to use cornea-derived extracellular matrix hydrogels for corneal tissue engineering; however, no studies have investigated its application in corneal ectasia. In this study, we have first developed an animal surgical model that mimics a few specific phenotypes of ectatic cornea. Later, we investigated the potential of decellularized cornea matrix hydrogels (dCMH) from both human and bovine sources in increasing the thickness of the cornea in the developed surgical model. Our data advocate that surgical stromal depletion can be followed to establish ectatic models and can also provide information on the biocompatibility of materials, its integration with native stroma, degradation over time, and tissue remodeling. We observed that dCMH from both sources could integrate with ectatic thin corneal stroma and helps in regaining the thickness by regenerating a reasonably functional and transparent stroma; however, no significant difference was spotted between the dCMH made from human and bovine corneal tissue sources. Hence, this study is a promising step toward developing a non-invasive technique for the treatment of corneal ectasia by using dCMH.