Autoimmune uveitis is a group of intraocular inflammatory disease that potentially leads to vision loss. We previously demonstrated that, using experimental autoimmune uveitis (EAU) mouse model, mucosal associated invariant T (MAIT) cells are required for mitigation of clinical symptoms and maintaining vision function. To elucidate the mechanisms, we performed histological analysis of retina in Mr1–/– mice and B6CAST mice after EAU induction. We found that severe inflammation around optic nerve was observed inMr1–/– mice but not B6CAST mice. RNA-seq analysis using retina of EAU mice revealed that decreased expression of genes involved in tissue repair (Col9a1, Col2a1, Ctgf, Pdgfra) and nerve regeneration (Rassf10, Fzd9) in Mr1–/– mice. Inflammations around optic nerve of EAU-induced C57BL/6 mice were affected by oral administration of antibiotics. Agonistic MAIT cell activity of feces homogenates from EAU-induced C57BL/6 mice were different depending on spectrums of antibiotics. These results demonstrate that MAIT cells are one of key players to maintain homeostasis in the retina responsible for vision function and microbiota may be involved in MAIT cell-dependent immune responses in the eye.