Sodium Tanshinone IIA Sulfonate, the chemical modification product of Tanshinon IIA (STIIAS) is widely used in clinical treatment of angiocardiopathy, and the preparation of reference compounds of related substances for quality control is necessary. A method for separating three related substances from the bulk drug of STIIAS with high-speed counter-current chromatography (HSCCC) was developed. A solvent system composed of chloroform–n-butanol–methanol–water (17:0.3:14:9) was used and 0.5% saturated ammonium acetate aqueous solution was added to depress the emulsification in order to enhance sample loading capacity. Twelve related substances were identified in the bulk drug by HPLC-DAD and liquid chromatography/multistage tandem mass spectrometry (LC–MS n ). Among them, three compounds were prepared and confirmed with 1 H NMR, one was identified without pretreatment, and seven components were identified after HSCCC enrichment since the contents of them were too low to be detected through direct LC–MS n injection. This research successfully broadened the application of HSCCC and introduced it to the field of impurities preparation of chemical medicine.