The problem of noise and baseline drift is a hot topic in infrared spectral harmonic detection system. This paper presents a new algorithm based on wavelet transform Mallet decomposition to solve the problem of eliminating a variety of complex noise and baseline drift in the harmonic detection. In the algorithm, the appropriate wavelet function and decomposition level were selected to decomposed the noise, baseline drift and useful signal in the harmonic curve into different frequency bands. the bands’ information was analysed and a detecting band was set, then the information in useful frequency was reserved by zeroing method of treatment and the coefficient of the threshold. We can just use once transform and reconstruction to remove interference noise and baseline from double-harmonic signal by applying the wavelet transform technique to the harmonic detection spectrum pretreatment. Experiments show that the wavelet transform method can be used to different harmonic detection systems and has universal applicability.