Huatuo reconstruction pill (HTRP) is a traditional Chinese medicine prescription that mainly treats for hemiplegia and postoperation of brain stroke. Existing pharmacological studies have previously shown that HTRP could inhibit in vitro thrombosis, delay platelet adhesion, dilate blood vessels, and improve the microcirculation disturbances. In this paper, we chiefly concerned about the potential targets of HTRP and tried to figure out the active components of it. Computer-aided drug design method was emploied to search for the active components and explain the mechanism between the targets and the small molecules at molecular lever. The potential targets of this compound pharmaceutics were searched through relevant pharmacological studies and three pharmacophore models which involved the platelet activating factor (PAF) receptor, the angiotensin converting enzyme (ACE) and the 5-hydroxytryptamine receptor (5-HT2A) were constructed by Discotech method of Sybyl. Thus, the candidate compounds which agreed with the pharmacophore models were obtained by the virtual screening to the known ingredients of HTRP. Based on that, sequence and structure prediction of the unknown targets were realized by homology modeling which were used for molecular docking with those candidate compounds. Results showed that three compounds, which may prove to be valid to these targets, got higher scores than the existing corresponding inhibitors after molecular docking, including ferulic acid, onjixanthone I and albiflorin. And the three molecules may refer to the singificant substances to the total compounds of HTRP which were effective to the disease.