Infrared spectra of semen celosiae and semen celosiae cristatae were obtained directly, quickly and accurately by Fourier transform infrared spectroscopy (FTIR) with OMNI sampler. Continuous wavelet transform was used to extrude local region of infrared spectra of semen celosiae and its confusable varieties. The difference of infrared spectra between semen celosiae and semen celosiae cristatae was extruded greatly. Accurate identification rate was improved greatly. Morlet wavelet, which can detect singular values of signal effectively, was selected as the mother wavelet. One-dimensional continuous wavelet transform was implemented for the infrared spectra of semen celosiae and its confusable varieties. The difference between semen celosiae and semen celosiae cristatae was observed at all scales in the wavelet domain. An optimal scale, at which the difference between semen celosiae and semen celosiae cristatae was the most obvious, was selected to identify semen celosiae and semen celosiae cristatae. The results show that it is effective to apply continuous wavelet transform on the basis of FTIR to identify the traditional Chinese medicinal materials, which are the same genus but different species.