Supercritical fluid extraction (SFE) was used to extract shionone from Aster tataricus L. f. The effect of various parameters, i.e., temperature, pressure and sample particle size on yield was investigated with an analytical-scale SFE system to find the optimal conditions. The process was then scaled up by 50 times with a preparative SFE system under the optimized conditions of temperature 40 °C, pressure 30 MPa, and a sample particle size of 40–60 mesh. Then preparative high-speed counter-current chromatography was successfully used for isolation and purification of shionone from the SFE extract with a two-phase solvent system composed of n-hexane-methanol (2:1, volume ratio). The separation produced a total of 75 mg of shionone from 500 mg of the crude extract in one step separation with the purity of 98.7%, respectively, as determined by high-performance liquid chromatography (HPLC) and 92% recovery. The structure of shionone was identified by electrospray ionization-mass spectrometry (ESI-MS), hydrogen-1 nuclear magnetic resonance (1H-NMR), and carbon-13 nuclear magnetic resonance (13C-NMR).