Lotus leaves have the dual identity of medicine and food homology as included in the Chinese Pharmacopoeia. Nuciferine is the major bioactive component which is highly abundant in the leaves of Nelumbo nucifera Gaertn. Nuciferine has been shown to potentially improve energy metabolism and protect neurons in cerebral ischemia. However, the mechanisms underlying the protective effects of nuciferine on acute ischemic stroke (AIS) are still unclear. Metabolomics was used for uncovering the underlying therapeutic mechanism of nuciferine in AIS with the help of ¹H NMR. The rat model of AIS was generated by the occlusion of the middle cerebral artery (MCAO). After treatment with nuciferine, several indexes of oxidative stress and inflammation, such as total antioxidant capacity (T-AOC), total glutathione/oxidized glutathione (GSH/GSSG), malondialdehyde (MDA), superoxide dismutase (SOD), tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) were significantly improved, and some metabolic biomarkers (histidine, glycine, glycerol, serine, tyrosine, lysine, choline, etc.) were significantly regulated. Bioinformatic analysis demonstrated that these biomarkers and the derived genes (myeloperoxidase, catalase, etc.), fatty acid and amino acid metabolisms and 9 key metabolic pathways were involved in the nuciferine activity, which indicated the potential therapeutic mechanisms of nuciferine in AIS.