Differential optical absorption spectroscopy (DOAS) is a commonly used atmospheric pollution monitoring method. Denoising of monitoring spectral data will improve the inversion accuracy. Fourier transform filtering method is effectively capable of filtering out the noise in the spectral data. But the algorithm itself can introduce errors. In this paper, a chirp-z transform method is put forward. By means of the local thinning of Fourier transform spectrum, it can retain the denoising effect of Fourier transform and compensate the error of the algorithm, which will further improve the inversion accuracy. The paper study on the concentration retrieving of SO2 and NO2. The results show that simple division causes bigger error and is not very stable. Chirp-z transform is proved to be more accurate than Fourier transform. Results of the frequency spectrum analysis show that Fourier transform cannot solve the distortion and weakening problems of characteristic absorption spectrum. Chirp-z transform shows ability in fine refactoring of specific frequency spectrum.