Abstract: OBJECTIVE To study on the differences of chemical composition between extraction of Rhizoma Coptidis and Cortex Magnoliae extracted by ethanol together and single，with fringerprint technology. METHODS The extracts of Rhizoma Coptidis and Cortex Magnoliae extracted by ethanol together and single under the same process. The comparison was done under the different wavelengths and different brand columns, HPLC method determined the extract's fingerprint within the range of optimized conditions. RESULTS The ratio of compositions and its main chemical substances are different between the two extracts, and the extract rate of the main chemical substances are different, too. CONCLUSION There are some chemical substances and composition's ratio differences in the extracts of Rhizoma Coptidis and Cortex Magnoliae Officinalis by ethanol together and single.