A practical solution of qualitatively analyzing quaternary alkaloids in coptis-scute herb couple by electrospray ionization mass spectrometry(ESI-MS) was developed. Without the complicated pretreatment of sample, the active ingredients including berberine, palmatine, coptisine, jatrorrhizine, epiberberine, and columbamine were identified and some relative content changing rules of alkaloids in coptis-scute couple were summarized in this article. The overall profiles of the complex extracts were obtained. After adding an internal standard(rutaecarpine), semi-quantitative analysis was performed and the result indicates that the actual content of alkaloids was decreased by increasing the amount of scute. Based on the data obtained by high-performance capillary electrophoresis(HPCE), the feasibility of semi-quantitative analysis by ESI-MS was further proved. A practical solution of qualitatively analyzing quaternary alkaloids in coptis-scute herb couple by electrospray ionization mass spectrometry (ESI-MS) was developed. Without the complicated pretreatment of sample, the active ingredients including berberine, palmatine, coptisine, jatrorrhizine, epiberberine, and columbamine Were identified and some relative content changing rules of alkaloids in coptis-scute couple were summarized in this article. The overall profiles of the complex extracts were obtained. After adding an internal standard(rutaecarpine), semi-quantitative analysis was performed and the result indicator Based on the data obtained by high-performance capillary electrophoresis (HPCE), the feasibility of semi-quantitative analysis by ESI-MS was further proved.