To report a rare case of Molybdenum Cofactor Deficiency with novel ocular manifestations. This is a case study of a 6-year-old boy who initially presented with conjunctival hyperemia and ocular pain of the left eye. Medical history revealed refractory convulsion, global developmental delay, microcephaly, feeding difficulties, aphasia, and spastic quadriplegia, as well as pathogenic MOCS2 mutations, indicating the diagnosis of molybdenum cofactor deficiency (MoCD). This case report highlights detailed ocular manifestations of late-onset MoCD-B, ectopia lentis of bilateral eyes, spherophakia, hyperemia, secondary glaucoma, cyclodialysis, and retinal detachment of the left eye, which will help further understanding of MoCD. MoCD as a rare genetic disease is tend to be easily neglected. The ophthalmic examination could provide important evidence for early diagnosis.