To explain the scientific connotation of the rational compatibility of Chinese herbal medicine based on the HPLC analysis, and discuss the effects of compatibility regularity of Rhizoma Atractylodis and Cortex Phellodendri herbs on pharmacodynamic substance. Methods:The linear relationship was analyzed by HPLC and the sample recovery test was used to investigate the preciseness of HPLC. HPLC finger-print: berberine and phellpdendrine comparison liquor, and Atractylodes rhizome and Cortex Phellodendri were used to make the test solution by the proportion of 1:1, 1:2, 1:3, 0:1, 2:1, 3:1, 1:0, which were analyzed by HPLC finger-print. Results:1) The retention time of berberine and phellpdendrine in Atractylodes rhizome and Cortex Phellodendri test solution was consistent with external standard method of control products by HPLC chromatogram. 2) The linear relationship was good in the range of 1.024 to 10.24 μg. 3) The average recovery rate of sample recovery teste was 99.80%, and RSD was 2%, which showed that the sample recovery rate was good, and HPLC had a high conscientiousness. 4) In the different compatibility rules of Rhizoma Atractylodis and Cortex Phellodendri, the non common peak area was the highest with the ratio of 3:1 compatibility to 10.62%, followed by 1:1, the proportion of compatibility was 8.06%. Conclusion:The effect of 3:1 compatibility proportion of Atractylodes rhizome and Cortex Phellodendri has the minimum effect on berberine, and Cortex Phellodendri has a good pharmaceutical effect, indicating the compatibility and drug dose play an important role in giving full play to the effects of the drugs.