Carbodiimide cross-linked amniotic membrane (AM) can potentially serve as an artificial corneal epithelial stem cell niche in ocular surface wound healing. For the first time, this study was performed to investigate the relationship between nanostructure and functionality of carbodiimide cross-linked AM tissues as limbal epithelial cell (LEC) scaffold biomaterials. The triple-helical molecular conformation of AM collagen was checked after chemical treatment for varying cross-linking durations (1-4 h). Our data indicated that the unraveling of the helical structure into a more random globular state is accompanied by an increase in the cross-linking index of AM samples. The cross-linker-mediated alterations in tissue ultrastructure and substrate nanotopography of these proteinaceous matrices were confirmed by transmission electron and atomic force microscopy studies. With increasing treatment time, the chemically cross-linked AM possessed larger nanofiber diameter and exhibited rougher texture. Marked increases in the water content, light transmittance, and resistance to enzymatic degradation were found, probably due to collagen fibril aggregation in biological tissues. All the test AM materials were not toxic to the human corneal epithelial cell cultures and retained anti-inflammatory activity, indicating the tolerability and safety of carbodiimide (i.e., a zero-length cross-linker). In addition, the enhanced LEC growth and increased p63 and ABCG2 gene expressions were significantly noted on the AM samples with greater cross-linking degree. In summary, the findings reported in this paper suggest that a specific limbal epithelial stem cell-biomaterial interaction may occur in response to biophysical cue such as nanostructure of carbodiimide cross-linked AM matrix.