Xin-Ke-Shu (XKS), a traditional Chinese medicine (TCM) preparation, has been widely used for treatment of coronary heart disease (CHD) in China. However, the active constituents of XKS and their interactions with targets remain unclear. In this study, we assessed two docking programs, LibDock and AutoDock, by calculating the root-mean-square deviation (RMSD) of X-ray structure reproduction and the enrichment factor (EF) in virtual screening; both proved to be practical in our protein-ligand complex systems. Moreover, the combined use of the two programs yielded better EFs for each target. We therefore used a combination of the two programs to investigate the interactions of the 51 chemical constituents identified from XKS with five CHD targets, namely peroxisome proliferator activated receptor γ (PPAR-γ), angiotensin-converting enzyme (ACE), hydroxymethylglutaryl coenzyme A receptor (HMGR), cyclooxygenase-2 (COX2), and thrombin. The docking results suggest that pueroside A, pueroside B, salvianolic acid A, and salvianolic acid C can interact with two or more targets, and the other eight compounds may be potent for at least one of the five targets. In this research, we propose a strategy for studying TCM preparations, and suggest that XKS has a multi-target effect on CHD.