Myocardial ischemia (MI), a condition in which the heart is unable to function due to insufficient blood and oxygen supply, is a major cause of death from coronary heart disease (CHD). Yiqi Tongluo capsule (YTC) is a Chinese patent drug which commonly used for treatment of MI in clinic. However, the related active components of YTC for treatment of MI were still uncovered. This paper is aimed to study the quality markers (Q-markers) of YTC and further optimize the extraction process of YTC based on Q-markers, providing research foundation for the further modern pharmaceutical preparations of YTC. We firstly used UPLC-QTOF-MS to analyze the constituents of YTC absorbed in blood, then isoprenaline (ISO) induced H9c2 cell model was used further screen the active constituents with protective effects on cardiomyocytes. After that, the orthogonal table (L9 (34)) was used to optimize the extraction process with three levels of 4 factors (water addition, immersion time, extraction time and decoction times). Finally, the HPLC fingerprint of 15 batches of optimized YTC was established. In our present study, a total of 33 components were identified in YTC, of which 10 components were absorbed in blood. Among the 10 components, 8 compounds had significant protective effects on ISO stimulated H9c2 cells, including Paeoniflorin, Ferulic acid, Calycosin, Senkyunolide A, N-butylphthalide, Z-ligustilide, LevistilideA, and Astragaloside IV, which were considered as the Q-markers of YTC. The optimized extraction process based on Q-marker as follows: soaking 1 h, then adding 8 times water to extract 3 times by decoction, each extraction lasts 1.5 h. The HPLC fingerprint of optimized YTC was established with 15 batches of YTC samples, and the optimized YTC samples has no significant toxicity to the heart, liver, spleen, lungs, and brain tissues of rats.