In the present study, combined with external standard method, second derivative as well as curve-fitting equation, the infrared spectroscopy techniques were applied to research the discrepancy of paclitaxel content among different parts of them repectively as well as the differences of infrared spectral character between Taxus Media(T. Media) and Taxus Mairei (T. Mairei). The results showed: (1) The band around 1 516, 1 371, 1 244, 1 109 and 773 cm-1 was markedly enhanced when paclitaxel standard sample was added by more than 0.004 5 mg to original traditional Chinese materials, in addition, in infrared fingerprint area, the second derivative spectra show that there was good corresponding peak between traditional Chinese materials and standard paclitaxel sample around 1 371, 1 315, 1 244, 1 143, 1 106, 1 070, 1 022 and 773 cm-1, furthermore, the intensity of above character band would increase accompanying with increased standard paclitaxel sample. So, the band character around 1 371, 1 315, 1 244, 1 143, 1 106, 1 070, 1 022 and 773 cm-1 could be used to evaluate paclitaxel content of T. media and T. mairei; (2) Around 1 800～700 cm-1, IR spectral features suggest that two kinds of Chinese yew had quite similar infrared vibration character, but when Gaussian function was applied to decompose the band around 1 058 cm-1, the result demonstrated that the T. media were decomposed with 8 while T. mairei were only decomposed with 7 component bands. (3) Second-derivative and curve-fitting equation analysis demonstrated that there were certain differences of paclitaxel content between T.media and T.mairei as well as different parts of them. Specifically, the paclitaxel content of T. media was higher than T. mairei, while the paclitaxel content in leaf of T. media was highest, on the contrary, the paclitaxel content in root of T. mairei was highest when comparing the content among the different parts of T. media and T. mairei respectively. Therefore, above methods could be quickly analyze and evaluate the differences of paclitaxel content between T. media and T. mairei as well as the different parts of them.