To develop an effective and rapid method for the preparation of ergosterol from a strain of Paecilomyces hepialid, the ethyl acetate extract of the mycelia was injected into a high-speed counter-current chromatograph (HSCCC) directly, and eluted with different solvent systems. The result showed that the solvent system composed of n-hexane-ethyl acetate-methanol-water (6: 1.7:6:0.3, v/v/v/v) was the best. The lower phase was used as the mobile phase and performed at a flow rate of 2 mL/min, while the apparatus rotated at 850 r/min, and detected at 280 nm. The prepared ergosterol was identified with ultraviolet detection (UV), high resolution mass spectrometer (HEMS) and standard, and its purity was 99.2% analyzed by high performance liquid chromatography. The established method is relatively simple, fast, and suitable for the large-scale isolation and separation of ergosterol.