An experimental evaluation on artificially contaminated clay soils with different amounts of heavy metals, which were then stabilized with two types of standard additives, was carried out. To examine the effect of those additives on the contaminated soils’ molecular system, vibrational (infrared) spectroscopy was employed. It is well known that contaminants in soil lead to inadequate engineering properties for contaminated soils. Thus, it can change the impact of these contaminants on clayey soil’s geotechnical characteristics soils over the mechanism of chemical stabilization that produces appropriate material that is preferable for construction uses. In this study, artificial polluted clay soils were prepared and then mixed with different proportions of heavy metals like (Pb and Zn) and stabilizers like quick lime CaO and ordinary Portland cement (OPC). The changes in the structure of soil molecular because of stabilizers and heavy metals were investigated based on Fourier Transform Infrared Spectroscopy (FTIR). The obtained results allow exploring the major vibrational modes in kaolin clay soil samples in which two active bands were observed at 3696.0 and 3620.0 cm⁻¹. These bands were related to the octahedral (OH) stretching vibrations and identified the kaolinite minerals. The bonding mode vibration of water-molecules (H–O-H) was discovered at 1638.0 cm⁻¹. It decreased with time because of the water consumption during the cement hydration and lime dissolution due to producing pozzolanic compounds, which are responsible for improving the strength properties of comminated soils. It was also investigated that heavy metals were at the absorbance band at 1384.0 cm⁻¹. So, it can be concluded from the importance of the applied FTIR test to evaluate the effect of stabilizers on the molecular structure of contaminated clay soils.