According to the X-ray fluorescence (XRF) spectral characteristics of heavy metals in soil, the application of XRF spectra de-noising using biorthogonal wavelet packet transform technology is analyzed. Wavelet pack decomposition and threshold setting are particularly discussed. Through spectra de-noising, the linear fitting relationship between concentration and intensity of Ni is meliorated. Experimental results demonstrate that this method can effectively overcome the noise interference and preserve characteristic spectra. This method is very useful to increase the accuracy of quantitative analysis, especially for analyzing trace elements in soil.