Immune-related ocular surface diseases, a group of diseases in which immune dysregulation damages the ocular surface, can induce uncontrolled inflammation and persistent epithelial defect, thus leading to the most severe forms of acute keratoconjunctivitis, dry eye disease, epithelial keratitis, stromal ulceration, and corneal perforation. As these diseases are often refractory to treatments, they have a threatening impact on the vision and life quality of patients. This review summarizes the current literature regarding the clinical application of sutured and self-retained cryopreserved amniotic membrane (AM) in treating Stevens–Johnson syndrome/toxic epidermal necrolysis, ocular graft-versus-host disease, Sjögren's syndrome, Mooren's ulcer, and peripheral ulcerative keratitis. Current evidence supports the safety and effectiveness of AM, especially self-retained cryopreserved AM, in decreasing ocular surface inflammation, promoting corneal epithelial and stromal healing, improving visual acuity, and preventing sight-threatening complications. Future studies are still required to validate the above findings and explore the varied application methods of AM to improve the clinical efficacy in maintaining ocular surface health.