In the present paper a method for identifying and evaluating traditional Chinese medicine (TCM) Jinkuishenqi pill and Guifudihuang pill samples is proposed. Mathematical statistics was applied to analyze the dual index sequences of infrared fingerprint spectra of components extracted from Jinkuishenqi pill and Guifudihuang pill samples with water, then the grade sequences were determined and the first and second clusters were performed based on these grade sequences. As a results, the most similar sample groups of different samples were also obtained. The Jinkuishenqi pill and Guifudihuang pill samples can be distinguished accurately with the most similar sample groups. The method put forward is new and effective to identify and evaluate combinational TCM quantitatively.