A fingerprint analysis of amino acids composition of Siwu decoction by HPLC was established and the different combination of HPLC conditions on amino acid composition was explored. The samples was treated by pre-column derivatization with 2,4-dinitrofluorobenzene and then analyzed by gradient elution with N, N-dimethylformamide-0.025 mol/L sodium acetate (1:100, with 36% acetic acid adjust pH=6.0)- acetonitrile at the flow rate of 1.0 mL/min on a Kromasil C-18 (250×4.6 mm×5 μm) column at 40 ℃.The UV detection wave length was set at 360 nm and the injection volume of samples was 10 μL . The analysis time was 70 min. 17 Co- possessing peaks were selected as the fingerprint peaks, among which 13 kinds of beneficial amino acid composition were identified. The results showed the similarity for 10 batches was above 0.97. Effect of herb components on fingerprints for the amino acid in decreasing sequence was Radix angelicae sinensis, Radix rehmanniae praeparata, paeonia lactiflora pall and Rhizoma chuanxion. The characteristic fingerprint of amino acid components can be used for the quality control of Siwu decoction, providing a reference for the research of the changes of chemical composition of Traditional Chinese medicine compatibility.