Strabismus is a common type of eye movement disorders, which is characterized by ocular misalignment and binocular visual dysfunction. Alignment relies on the normal structure and function of the visual and oculomotor systems. Any abnormalities of these regions may lead to strabismus. With the application of neurophysiological techniques and radioautography in the early years, the impairment of primary visual cortex was found, including decreased number of binocular neurons and metabolic changes of ocular dominant column. In recent years, the progress of functional magnetic resonance imaging has promoted to find more functional changes in human strabismic brains, especially in extrastriate cortex. In addition to the structural impairment of cerebral cortex and intercortical connections, functional remodeling of cerebral cortex was also observed in patients with strabismus. Besides, studies based on voxel-based morphometry and diffusion tensor imaging provided more precise anatomical evidence for human brain abnormalities. To provide reference for further studies, we review the current literature on functional and morphological deficits within brain regions in strabismus.