In China, Astragali Radix (Huangqi, HQ) has been extensively applied as a bulk medication. Currently, two forms of HQ are available on the market: wild-simulated HQ (WHQ) and transplanted HQ (THQ), However, it is uncertain whether the two are equally effective. This study compared the differences in their effects by investigating the efficacy of the herbal combination of Astragali Radix and Salvia miltiorrhiza (Huangqi-Danshen, HD) in the prevention of focal cerebral ischemia (FCI) rats. To achieve the more accurate differential metabolites related to FCI, we proposed a tissue-targeted metabonomic study in conjunction with a novel screening strategy based on ultra-high performance liquid chromatography coupled with the quadrupole-Exactive mass spectrometry (UHPLC-Q Exactive MS). The appropriate thresholds of four screening factors (variable importance in the projection (VIP), log2 absolute value of fold change (|log2(FC)|), -In(p-value) and ǀp(corr)ǀ) and their best combination were determined by comparing R2X, R2Y, and Q2 of the orthogonal to partial least squares discriminant analysis (OPLS-DA) models. Eleven metabolites were significantly screened and associated with focal cerebral ischemia through the novel metabolomics strategy. The transplanted HD (THD) had a better callback effect on these eleven metabolites compared with the wild-simulated HD (WHD), especially γ-L-Glutamyl-l-glutamic acid, proline, maleic acid, and S-(Formylmethyl)glutathione. Additionally, the optimal WHD and transplanted THD doses were found to be medium and high. Pathway analysis revealed that middle-dose WHD and high-dose THD largely participated in four and six metabolic pathways, respectively. The results further revealed that THD was better than WHD against focal cerebral ischemia. These findings provided a unique perspective on an integrated comparison of the efficacy difference between WHQ and THQ. In addition, the tissue-targeted metabonomic study gave us new insights into the pathological mechanism of focal cerebral ischemia.