Abstract Smectite, a major barrier material for contaminants in Earth’s critical zone, is a layered aluminosilicate mineral with cis-vacant (cv) and trans-vacant (tv) configurations. High-temperature transformations of smectite are directly related to the smectite’s thermal reactions. However, the precise thermal reaction mechanism and thermally induced structural transition of cv and tv smectites remain debated. In this study, we systematically investigated the mechanism of thermal reactions of cv and tv smectite models using reactive force field (ReaxFF) molecular dynamics. We explored the deprotonation and the intralayer dehydration steps of cv and tv smectites at 700K and 900K. The results revealed that the dehydroxylation reaction of cv smectite exhibited more difficulty than tv smectite at 700K, while demonstrating easier at 900K. Furthermore, it is found that the dehydroxylated cv and tv smectites evolved to a consistent structure spontaneously. Our findings further confirmed that cv smectite has a higher dehydroxylation temperature than tv smectite and thus provided a theoretical basis for distinguishing cv and tv smectites using thermogravimetric analysis (TGA). Moreover, we gathered TGA data of smectites from different regions, confirming that montmorillonites have cv structure and almost all smectites from China (over 11 provinces) are cv. This study provides a molecular-level understanding of the thermal reaction mechanisms of smectites and a physical basis for further study and application of smectites.