Two-dimensional hetero-spectral correlation analysis has been widely used for the interpretation of spectral changes of humic substances involved in various environmental processes. However, when three different types of spectroscopies are utilised, only a pairwise correlation can be achieved. In order to overcome this problem, a novel method of three-dimensional hetero-spectral correlation analysis with scaling technique was developed in this study, which can further establish a direct correlation between three different types of spectroscopies, including FTIR, C CP/MAS NMR, and XPS. The proposed method was applied to the fingerprint identification of undissolved humic acid functional groups for Cr(vi) retention, which is one of the most important points for understanding the migration and transformation of Cr(vi) in a subsurface environment. The results indicated that mainly free and dissociated carboxylic groups, phenolic groups, and polysaccharide participated in the reaction with Cr(vi), and these functional groups were mainly located at aromatic domains. Besides, the variations of functional groups were related to the reduction of Cr(vi), and the reduced Cr(iii) mainly bound to aromatic domains. The successful application of the proposed method demonstrated that it can serve as a promising tool for further investigations concerning more complicated environmental processes and even other scientific fields by supplying more detailed, reliable and visualised spectral information.