NaoMaiTong (NMT: Radix et Rhi-zoma Rhei, Radix Ginseng, Radix Puerariae, and Rhizoma Ligustici Chuanxiong as 9: 9: 6: 6) is a traditional Chinese medicine prescription for treating ischemia cerebral apoplexy. In this work, four cell injury models of ischemic stroke were establish, namely hypoxic injury, glutamate damage, injury of potassium chloride and hydrogen peroxide damage model. The protective effects of NMT and its single herbs-containing sera of different time points on PC12 cell damage were evaluated respectively, and the corresponding efficacy-time curves were drawn. Cell viability was measured by MTT (3-(4,5)-Dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide) assay. Furthermore, an statistical methods of support vector machine (SVM) were used to establish the correlation between concentration-time-efficacy for the first time. These results revealed that NMT-containing serum has obvious protective effect on the four injury models and can significantly improve cell viability. The PK-PD correlation between fifteen ingredients in the NMT compound with four model efficacy indexes indicated that rhein, puerarin, and 3'-methoxy puerarin might be the most important constituents controlling the pharmacological effects of NMT. The study suggested that these fifteen components are likely to be the material basis of NMT and recommended to increase the amounts of Pueraria in the NMT compound. That provided the scientific basis and demonstration for the research of efficacy material base of Traditional Chinese Medicine (TCM).