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Loess soil is a kind of widespread soil type in northwest China. Human engineering activities such as mining have caused numerous problems related to heavy metal pollution in soils, which threaten people’s health. The band formation mechanism of the near-infrared (NIR) spectral features in loess soils forms the theoretical basis for the study of the soil environment by hyperspectral remote sensing. Some NIR features of loess soils will shift because of the variations of the soil composition and microstructure after they adsorb heavy metal cations. In this study, we focused on the heavy metal adsorption of the illite, smectite, and illite−smectite (I/S) mixed layer in loess soils; evaluated the pollution by Nemerow indexing; applied X-ray diffraction (XRD), mid-infrared (MIR) spectral analysis, and inductively coupled plasma mass spectrometry (ICP-MS); and carefully observed the shift behavior of the MIR and NIR features. Then, the NIR bands were assigned to MIR bands according to the vibration behavior. Furthermore, the relationships between the NIR band positions and the six heavy metal cations as well as the Nemerow index were investigated via multiregression and simple linear correlation methods. Finally, the relationship obtained from the experiments was analyzed using the physical and chemical mechanisms of the heavy metal cations in the clay minerals. These findings may benefit the application of NIR and remote sensing techniques for detecting heavy-metal-polluted soils.