Objective To observe the structure of the visual organ and functional development of marine medaka and to provide a theoretical basis for further studying its behavior. Methods The structure of visual organ of marine medaka was examined, with emphasis on the variations of its eyeball and retina. Results The medaka visual organ developed very rapidly. At the embryonic period, the pigment layer of the eyeball appeared, and there already had a significant eye area. At the first day, the structural development of the eyeball and retina were basically completed. At the 6th day, there was a significant difference of pigment layer and photoreceptor layer between light and dark vision. At the 23th day, the retinal structure was greatly changed, which can explain the reason about the change of medaka from the floating stage to the benthic stage. During from 9 to 14 month-old, the thickness of all layers in the retina decreased, indicating that the vision was degraded. Meanwhile, the kernel layer differentiation was obvious, as vertebral cells showed photoreceptor layer structure closely inlaid with rod cells, that medaka has good light sensitivity and strong visual acuity. The rapid development of medaka visual organ can be recognized as it needs to adapt the surroundings and to keep the life events such as feeding. Conclusions The development process of the visual organ of marine medaka is obvious and can provide a theoretical basis for further study of its behavior, and it may be a good experimental method for studying other related species.