To analyze the main chemical components from compatibility of Chaihu and Huangqin by HPLC and to explain the scientific connotation of rational compatibility. Methods:High performance liquid chromatography (HPLC) fingerprint was used for test precision of HPLC instrument. Repeatability of HPLC fingerprint method was test and sample stability was also tested. HPLC fingerprint:Ten batches of Chaihu and Huangqin were taken and 5 μL solution was prepared according to the conditions of chromatography and the chromatogram. Fingerprint of compatibility of Chaihu and Huangqin was determined and recorded. Results:1) The peak areas in the precision test over 5% of the total peak area were No. 22, 30, 36 and 47. 2) The similarity of the main color peaks in the repeatability test and the stability test was greater than 0.99, which showed good repeatability and stability. 3) The total peak areas of the HPLC fingerprint of the ten batches of Chaihu and Huangqin greater than the total peak area were No. 22, 30, 36, and 47 and the similarity of the chemical compatibility of the ten batches of Chaihu and Huangqin was above 0.99, showing a good similarity. 4) Most substances in the decoction of Chaihu with Huangqin came from Chaihu and chromatographic peak after 45 min was the characteristic peak of Chaihu, while characteristic peak of Huangqin mainly appeared during 15~45 min. The main chemical components were saikosaponin a and baicalin. Conclusion:The main components in decoction of Chaihu and Huangqin were saikosaponin a and baicalin.