A precise investigation on the efficacy of multicomponent drugs against HF using the signature biomarkers-oriented approach was developed in this study and applied to a conventional drug for cardiac disease, YiXinShu (YXS). Based on in vitro and in vivo efficacy evaluation of YXS against HF and with the aid of proteomics and network pharmacology approaches, specific signatures regulated by YXS against HF were confidently confirmed. YXS may show distinctive treatment features for those HF patients showing the elevation of fatty acid-binding protein 3 and cytoskeleton-associated protein 5, as well as other classical HF biomarkers. This study provides the first precise investigation of the efficacy of multicomponent drugs against HF and offers a smarter and low-cost approach for precise medicine in the management of heart failure (HF).