The high intra-class variability of rock spectra is an important factor affecting classification accuracy. The discrete wavelet transform (DWT) can capture abrupt changes in the signal and obtain subtle differences between the spectra of different rocks. Taking laboratory spectra and hyperspectral data as examples, high-frequency features after DWT were used to improve the discrimination accuracy of rocks. Various decomposition levels, mother wavelet functions, and reconstruction methods were used to compare the accuracy. The intra-class variability was measured using the intra-class Spectral Angle Mapper (SAM). Our results show that the high-frequency features could improve the discrimination accuracy of laboratory spectra by 13.4% (from 46.5% to 59.9%), compared to the original spectral features. The accuracy of image spectra in two study areas increased by 8.6% (from 68.3% to 76.9%) and 7.2% (from 81.3% to 88.5%), respectively. Haar wavelets highlighted the spectral differences between different rocks. After DWT, intra-class SAM reduced and intra-class variability of rocks decreased. The Pearson correlation coefficient indicated a negative correlation between intra-class variability and overall accuracy. It suggested that improving classification accuracy by reducing intra-class variability was feasible. Though the result of lithological mapping still leaves room for improvement, this study provides a new approach to reduce intra-class variability, whether using laboratory spectra or hyperspectral data.