Ischemic stroke is one of the leading causes of death worldwide, and effective treatment strategies in the chronic phase of this disease remain insufficient. Homeostasis of metals in the brain plays an important role in maintaining normal brain function. However, the dynamic spatial distributions of iron, zinc, calcium, potassium, and copper in a rat brain following ischemic stroke and the association between structural distribution and function remain to be elucidated. In this study, we used a synchrotron radiation-based micro-X-ray fluorescence technique to image element mapping changes in special rat brain regions after ischemic stroke, showing the distribu-tion characteristics of iron, zinc, calcium, potassium, and copper. We demonstrated, for the first time, the consistent dynamic spatial distributions of metal elements at a series of time points (3 h, 4.5 h, 6 h, 12 h, 1 d, 3 d, 5 d, 7 d, 10 d, 14 d, 28 d) after brain ischemia, which revealed that the homeostasis of iron, zinc, calcium, potassium, and copper in the brain was disturbed with distinctive change trends, providing clear insights in understanding the underlyingpathogenesis of stroke from a novel perspective, thus lay-ing the foundation of further developing new drug targets for stroke treatment.