For the overlap of the absorption spectrum of NH3 and SO2 from 196 nm to 214 nm, based on differential optical absorption spectrometry and fast Fourier transform to measure concentration of gases, a method that detecting these two gases simultaneously at two wave length bands is proposed. The crosstalk effects between the characteristic spectrum of NH3 and SO2 are solved. The interference of SO2 to NH3 which is caused by the nonlinearity of the absorption of SO2 with the increase of its concentration within 196~214 nm wavelength band is corrected, then the real concentration of NH3 are obtained. The signal to noise ratio is improved by empirical mode decomposition (EMD) noise reduction method. The measurement error of NH3 concentration is within ± 0.15 mL/m3 , ang the relative error is less than ±1.5%. The detectable concentration limit is 1.5 mL/m3. For SO2, the measurement error is within ±2 mL/m3, and the relative error is less than ±1%. The detectable concentration limit is 16 mL/m3.