[ Objective] The research aimed to get the optimized separation and purification conditions of the hirudin produced from Bacillus subtilis DB403 (pUBH5). [Method] Through the systemic pretreatment, preliminary chromatography and fine chromatography. [Result]The optimized separation and purification conditions were that: Supernatant was treated by trichloroacetic acid, then by ultrafiltration desalt and anion exchange chromatography. Strong anion Q F. F. was better than weak anion DEAE F.F. The proper balanced solution was Tris-HCI ( pH 8.0). The proper conductivity was 6 ms/cm. The maximum applied sample was 240 ATU/ml to matrix of strong anion Q F. F. This optimized procedure was magnified in strong anion exchange HiPrep 16/10Q with the 90% recovery and 70.2% purity. The purification of gel filtration of Sephacryl S-100 to hirudin was not relative to flow rate within certain scope. The application size of sample was 10 ml. The purity checked by HPLC was 95.1%, and the recovery was 93%, and the band of SDS-PAGE was single. [ Conclusion] The research provided the reference of the further industrialization separation and purification of hiruin.