Objective: To study on the differences of chemical composition between extraction of Salvia Miltiorrhiae Radix et Rhizoma and Carthami Flos extracted by water together and single, with fingerprint technology. Methods:The extracting solution of Salvia Miltiorrhiae Radix et Rhizoma and Carthami Flos were extracted by water together and respectively under the same process. The comparison was done under the different wavelengths and different brand columns and different mobile phase, HPLC method determined the extracting solutions fingerprint within the range of optimized conditions. Results:The ratio of compositions and its main chemical substances are same between the two extracting solution.Conclusion: some chemical substances and compositions ratio are same in the extracting solution of Salvia Miltiorrhiae Radix et Rhizoma and Carthami Flos extracted by water together and respectively.