Pathological angiogenesis in the eye is the most common cause of blindness in all age groups. In physiological and pathological cellular processes including angiogenesis, ion homeostasis is greatly affected. This study is to investigate the role of calcium ion in physiological and pathological angiogenesis in the retina, which is based on the results of ion mapping by time-of-flight secondary ion mass spectrometry (TOF-SIMS). We provided that calcium distribution is the most accordant to change with physiological vessel formation of development in the retina and pathological angiogenesis of oxygen-induced retinopathy (OIR), which is supported by ion mapping in retinal tissue using TOF-SIMS. In addition to anti-proliferative and anti-angiogenic activity of the calcium inhibitor on endothelial cells, retinal neovascularization of OIR was effectively inhibited by the calcium inhibitor. Calcium ion could play a crucial role in physiological and pathological angiogenesis in the retina. Moreover, TOF-SIMS could be a good method to simultaneously evaluate the changes of variable ions of the retina in biological processes.