A sensitive and simultaneous analytical technique for visualizing multiple endogenous molecules is now strongly required in biological science. Here, we show the applicability of a matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) system for getting chemically diverse metabolite profiles on a single-mammalian cell. This ultrahighly sensitive MALDI-MS technique enabled a spatially resolved detection of a broad range of metabolites including nucleotides, cofactors, phosphorylated sugars, amino acids, lipids, and carboxylic acids in normal mouse brain tissue with their unique distributions. Furthermore, a combination of MS imaging and metabolic pathway analysis of a rat transient middle cerebral artery occlusion model visualized a spatiotemporal behavior of metabolites in the central metabolic pathway regulated by an ischemia reperfusion. These findings highlight potential applications of an in situ metabolomic imaging technique to visualize spatiotemporal dynamics of the tissue metabolome, which will facilitate biological discovery in both preclinical and clinical settings.