Objective: To study the scutellaria and coptis in different proportions, the main active ingredient of baicalin, berberine dissolution rate changes and to explore the effect of traditional drug pair of scutellaria and coptis on the dissolution rate of active ingredient. Methods: Based on the clinic common used prescriptions of scutellaria with coptis, ratio of 1:0,1:1,1:2,1:3,2:1,2:3,3:1,3:2,0:1 was selected, after the water boiling reflux extraction, refining separation, various products were obtained for the test, under the optimized conditions of RP-HPLC analysis to compare chromatographic fingerprints and to examine the main component baicalin, berberine in aspects of relative peak area ratio of changes and compatibility relations. Results: Compatibility of Scutellaria baicalensis and Coptis at different proportions can influence the dissolution rate of baicalin, Berberine Hydrochloride. There was a non-linear relationship of dissolution rate of baicalin and Scutellaria baicalensis. The best ratio of scutellaria ratio was 3:1, the best compatibility ratio of coptis was 1:3. Conclusion: Different compatibility proportions of scutellaria and coptis will result in different dissolution rate of baicalin and berberine.