FTIR combined with EDS fingerprint spectra was first applied to the identification of two kind of traditional Chinese compound formulae-Yougui pill and Jisheng shenqi pills, which have the similar composition. The IR FPS of extraction of two kinds of pills extracted with chloroform were measured by liquid membrane method. The exclusively characteristic peak groups of these two kinds of formulae were theoretically established based on the Shapiro-Wilk W testing method，and the characteristic radicals and compound species corresponding to each characteristic peak were determined. Meanwhile, EDS fingerprint spectra of the two kinds of original powders were also measured which can reflect the element species and content information. Based on the three kinds of information (characteristic peak groups, radicals and compound species, different elements), Yougui and Jisheng shenqi pills were identified quickly, precisely and reliably. In this method, infrared fingerprint spectra possess the similar ability with chromatograph fingerprint spectra in identification of traditional Chinese compound formulae. The results show that the new visual comparison method is suitable for identifying traditional Chinese compound formulae with the same dosage-form and similar composition.