Scutellaria baicalensis Georgi flowers is rich in flavonoids resources but not effectively exploited. This study aimed to investigate the anti-aging effects and potential mechanism of Scutellaria baicalensis Georgi flowers extract (SFE). The chemical components of the SFE were analyzed by UPLC-MS and the anti-aging effects of SFE were investigated in d-galactose (d-gal) induced aging rats by behavior examination and biochemical indexes, and the potential anti-aging mechanism of SFE were explored by 1H NMR-based liver metabolomics. Chemical composition research showed that 19 flavonoids were identified in SFE, and pharmacological research showed that SFE could significantly ameliorate spatial learning and memory ability. SFE could significantly regulate malondialdehyde (MDA), superoxide dismutase (SOD) and advanced glycation end products (AGEs). It also ameliorated the pathological abnormalities in liver. Additionally, anti-aging mechanism of SFE showed that total of 10 potential biomarkers were found by metabolomics techniques, which involved in 6 metabolic pathways. Among them, SFE could significantly increased the levels of d-glutamine and d-glutamate. Furthermore, the levels of glutamine and glutamate, and the levels of the key amino acids, enzymes and final product in the synthesis process of glutathione (GSH) were quantitatively determined in the liver by commercial kits and enzyme-linked immunosorbent assay. These results indicated that regulation of the glutamine-glutamate metabolic pathway is involved in the anti-aging effect of SFE in d-gal induced aging rats.