Objective: To optimize clarification process of Gastrodiae Rhizoma extract with chitosan flocculating method. Method: HPLC was employed to determine the content of gastrodin with mobile phase of acetonitrile-water(3: 97) and detection wavelength at 220 nm.Taking clarification effect and solids content as indexes,on the basis of single factor tests,orthogonal design was used to optimize clarification process with the adding amount of chitosan,liquid concentration ratio,flocculation temperature and standing time as factors. Result: Optimal clarification procedure was obtained under these conditions:the adding amount of chitosan 0.15%,liquid concentration ratio 1.13 g·mL-1,flocculation temperature at 25 ℃,standing time of 10 h.The concentration of gastrodin was 65.93 g·L-1,solids content was 3.157%. Conclusion: This optimized process is feasible and economical with good clarification effect,which is suitable for purification of Chinese medicine extract.