Isosteviol sodium (STV-Na) was reported to possess significant protective effects on ischemic stroke in recent years. However, the protective mechanism of STV-Na against stroke was still unclear. In this work, an untargeted lipidomics approach based on the ultra high-performance supercritical fluid chromatography coupling with ion-trap and time-of-flight tandem mass spectrometry (UHSFC-IT-TOF/MS) was employed to investigate the lipid profiles of stroke rats with STV-Na treatment for the first time. The possible mechanism of STV-Na was further elucidated. The UHSFC-IT-TOF/MS-based method achieved a fast separation of various lipids within 9min with a qualified repeatability. Multivariate statistical analysis was used to show differences in lipid profiles induced by stroke and STV-Na treatment. The results showed a clear separation of the model group and the sham group, with the STV-Na group as well as EDA group located much closer to the sham group than the model group, which was consistent with the results of physiological and pathological assays, indicating the protective effects of STV-Na. Fifteen differential lipids that presented significant differences between the sham group and the model group were screened and identified. With the treatment of STV-Na, 15 differential lipids in stroke rats showed a tendency to the normal levels. Among them, 6 lipids were significantly reversed to the normal levels by STV-Na. The results of pathway analysis suggested the protective effects of STV-Na might be related to the regulation of several metabolic pathways including glycerophospholipid metabolism, arachidonic acid metabolism and sphingolipid metabolism. This work demonstrated that the UHSFC-IT-TOF/MS-based lipidomics profiling method was a useful tool to investigate the protective effects of STV-Na against stroke.