A FTIR spectrum fitting algorithm based on continuous wavelet transform is proposed. In calculating the factor of difference spectrum, the algorithm takes into account both the original spectrum and its continuous wavelet transformed spectra, which effectively overcomes the problem of reference peak selection and manual factor selection in most commercial software. The detailed discussions on wavelet scale, order and basis are included. The spectral fitting is performed on six wavelet basis functions and the obtained scale factor is used to quantify the content of liquor, and the corresponding mean absolute error ranges 0.047 to 0.072, the standard deviation ranges from 0.056 to 0.091. Experimental results show the CWT combined with least squares fitting provides an accurate and reliable new method for FTIR spectral substraction.