Complex amine metabolic disorders are implicated in ischemic stroke and can further exacerbate brain damage. Therefore, ameliorating their metabolic disorder would be an effective way to improve recovery from brain damage after ischemia/reperfusion (I/R) injury. In this work, the protective effects of Edaravone (Eda), Ginaton injection (Gin), and their combination (Eda+Gin) against cerebral I/R injury in a middle cerebral artery occlusion/reperfusion (MCAO/R) rat model were preliminarily investigated from the perspective of spatial metabolomics. Compared to single-drug treatment, the optimized combination treatment with Eda and Gin significantly decreased infarct volumes, improved neurological function, and inhibited neuronal damage and glial cell activation in MCAO/R rats. Also, combination treatment could prolong the blood circulation time of quercetin, ginkgolide C, and eight flavonoid glycosides compared to Gin treatment alone. More importantly, the spatial metabolic alterations of amine metabolites in MCAO/R rats before and after drug treatment were comprehensively interrogated using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) coupled with laser-assisted chemical transfer (LACT)-based on tissue chemical derivatization, such as amino acids, dipeptides, tripeptides, neurotransmitters, and the other amine metabolites. MALDI MSI results showed that the drastic metabolic disorders occurred in the cerebral cortex (CTX) and striatum (STR) and combination treatment exerted a better regulatory effect on the perturbed spatial amine metabolism. Therefore, combination treatment with Eda and Gin could significantly reduce ischemic brain damage and correct spatial metabolic disorders of amine metabolites, providing a potential treatment strategy for cerebral I/R injury.