The cornea is the outermost transparent layer of the eye that serves as a protective barrier and studying the cornea can be crucial for understanding human corneal diseases. Although several studies have examined the single-cell transcriptomic composition of the human cornea, its organoids have not been examined similarly. This study explained the transcriptomic cell fate of human cornea organoids and human donor corneas. The organoids harbor cell clusters that resemble cells of the corneal epithelium, stroma, and endothelium. Unlike the adult cornea where the largest cell population is stromal, the organoids contain large proportions of epithelial and endothelial-like cells. These corneal organoids offer a 3D model to study corneal diseases and integrated responses of different cell types. The dataset contains single cell RNA sequencing data.