The collagen with glycosaminoglycans such as chondroitin sulfate can potentially be used in many soft tissue engineering applications since the scaffolds mimic the structure and biological function of native extracellular matrix (ECM). In this study, we designed woven and aligned collagen-chondroitin sulfate mats by electrospinning method. The electrospun mats cross-linked with glutaraldehyde vapor at different times, the cross-linked mats became more biostable and were resistant to collagenase degradation. Cellular results with corneal epithelial cells showed that bioviability was reduced in cross-linked mats with glutaraldehyde. Characteristics such as high surface area of nanofibers, biodegradability, and orientation of fibers may maximize cell-ECM interaction and promote tissue regeneration faster than other conventional scaffolds. The cross-linked collagen-chondroitin sulfate electrospun mats can be used in tissue engineering, especially in soft tissue regeneration.