Neurological damage in glaucoma does not only limit to the eye, but also affects the central nervous system of the visual pathway. Functional magnetic resonance imaging provides a non-invasive method that can help to assess anatomical and functional changes of the central nervous system. This technology has been used in the investigations of nerve fiber damage, metabolic changes in visual cortex, and dysfunction of the visual system in glaucoma. Functional magnetic resonance imaging is introduced, and the progress in its application and prospect in glaucoma diagnosis were summarized in this paper.