Shengxian decoction, a traditional Chinese medicinal prescription, has been shown to alleviate doxorubicin‐induced chronic heart failure. This study established an ultra‐performance liquid chromatography‐quadrupole time‐of‐flight mass spectrometry method to separate and characterize the complex chemical compositions of Shengxian decoction, and the absorbed compounds in the bio‐samples of the cardiotoxicity rats with chronic heart failure after its oral delivery. Note that 116 chemical compounds were identified from Shengxian decoction in vitro, 81 more than previously detected. Based on the three‐dimensional data of these compounds, 28 absorbed compounds were confirmed in vivo. Network pharmacology and molecular docking experiments indicated that timosaponin B‐II, timosaponin A‐III, gitogenin, and 7,8‐didehydrocimigenol were recognized as the key effective compounds to exert effects against doxorubicin cardiotoxicity by acting on targets such as caspase 3, cyclin‐dependent kinase 1, cyclin‐dependent kinase 4, receptor tyrosine‐protein kinase erbB‐2, and mitogen‐activated protein kinase 1 in p53 and phosphatidylinositol 3‐kinase‐Akt signaling pathways. This study developed the understanding of the composition of Shengxian decoction for the treatment of doxorubicin cardiotoxicity, as well as a feasible strategy to elucidate the effective constituents in traditional Chinese medicines.