Abstract: Objective Extraction process of modified Xiongqiong decoction was researched and optimized on the basis of mice models of cerebral ischemia-reperfusion damages according to its material basis. Methods Six extraction processes of modified Xiongqiong decoction were explored according to modern references. Contents of active ingredients in the extracts were determined and protective effects of them on mice models of cerebral ischemia-reperfusion damages were observed. Optimum extraction process was selected according to determination of material basis and comparison of anti-cerebral ischemia. Results Active ingredients in the extract of the fifth extraction process is comprehensive relatively according to the integrated evaluation to volatile oil, walnut oil and ferulic acid. Extract of the fifth extraction process improved most obviously cerebral ischemia-reperfusion damages in all the extracts. Conclusion Model of "quality-efficacy" comprehensive assessment can guarantee effectiveness of Chinese medicine compound. The fifth extraction process has been confirmed to be optimum extraction process of modified Xiongqiong decoction preliminarily. However specific optimum parameters of the fifth extraction process need to be confirmed by a further study.