Selection of suitable labeled constituents is vital for the quality standardization of herbal medicines (HMs). However, discovery of labeled constituents that can account for the whole efficacy of original HMs is a challenging issue. Taking tanshinones extract (TE) as an example, a strategy to establish reasonable quality control method using effective compounds combination (ECC) as labeled constituents was proposed. The strategy consists of three core steps, including chemical profiling of TE, discovery and in vivo process research of ECC, and quality standardization based on ECC. Using this strategy, a combination of four tanshinones (tanshinones IIA, cryptotanshinone, tanshinone I and dihydrotanshinone I), which was as effective as TE in cell models and in a rat model of myocardial ischemia-reperfusion, was identified as ECC in TE. Furthermore, quality standardization of TE was established based on proposed ECC using single standard for determination of multiple components (SSDMC) method. In conclusion, the presently developed ECC-based approach not only offers new insight into the understanding of the holistic effects of HMs, but also provides efficacy-associated labeled constituents for quality control of botanicals.