To evaluate the effects of different compatibility of Mahuang decoction on the effective components of Semen Armeniacae Amarum and Radix Glycyrrhizae based on the fingerprint of Chinese herbal medicine. Methods:Amygdalin reference solution and glycyrrhizinic acid standard solution and the different combination of Mahuang decoction test solution were prepared. 8 types of different combinations of Mahuang decoction were orthogonally designed, and A-H mark was used to effective ingredients of Semen Armeniacae Amarum; A1-H1 was marked to active ingredients of Radix Glycyrrhizae in different combinations Mahuang Decoction. Finally, the similarity analysis was carried out, according to the similarity evaluation system 2004A of traditional Chinese medicine fingerprints proposed by the national pharmacopoeia committee, and the MATLAB software was used for data processing and statistics. Results:1) The chromatographic conditions of Semen Armeniacae Amarum and Radix Glycyrrhizae could separate the amygdalin and glycyrrhizic acid respectively. There was no other impurity peak, and the baseline was stable and comparable. 2) There was no significant difference in amygdalin of Semen Armeniacae Amarum in each different Mahuang decoction. The variance analysis showed that there was no significant difference (P>005) in Herba Ephedrae, Ramulus Cinnamomi, Radix Glycyrrhizae in Mahuang decoction with different compatibilities. 3) H1 with pure glycyrrhizin content was the highest in different combination of Mahuang Decoction, while the contents of A1 with glycyrrhizic acid in Mahuang decoction were the lowest. Herba Ephedrae, Ramulus Cinnamomi, Radix Glycyrrhizae in different combination of Mahuang Decoction decreased the content of glycyrrhizic acid in Mahuang decoction (P<005). Conclusion:Herba Ephedrae, Ramulus Cinnamomi and Radix Glycyrrhizae in different compatibility of Mahuang decoction had little significant effects on almond amygdalin; and they all decreased the contents of effective components of licorice of glycyrrhizic acid.