A multi-denoising method based on the empirical mode decomposition (EMD) is proposed to minimize the interference noises in the multi-pass absorption spectra. The denoising number is theoretically analyzed and determined. The CO2 spectral lines with different volume fractions detected by the direct absorption technology and wavelength modulation spectroscopy at second harmonic are denoised by the multi-EMD, and the results are compared with those by the denoising methods with multi-averaging and low-pass filtering. The results show that the interference and random noises can be effectively filtered by the multi-EMD denoising method. Moreover, the denoised signal amplitude has a good linear relationship with the volume fraction of the gas to detect, and the detection sensitivity of the whole system is up to 3.5 × 1 0-5. The spectral signals of CO2 standard gas at different pressures and temperatures are detected. After the multi-EMD denoising, the interference amplitudes of the spectral signals are reduced by about two orders of magnitude, but the signal to noise ratios are enhanced by about two orders of magnitude.