The formation of a unique microstructure of minerals on the surface of airless bodies is attributed to space weathering. However, it is difficult to distinguish the contributions of meteorite impacts and solar wind to the modification of lunar soil, resulting in limited research on the space weathering mechanism of airless bodies. The thermochemical reactivity of troilite can be used to distinguish the contributions of impact events and solar wind to the modification of lunar soil and provide evidence for space weathering of lunar soil. We examined the structure of troilite particles in the Chang’e-5 lunar soil and determined whether an impact caused the thermal reaction. Microanalysis showed that troilite underwent substantial mass loss during thermal desulfurization, forming a crystallographically aligned porous structure with iron whiskers, an oxygen-rich layer, and other crystallographic and thermochemical evidence. We used an ab initio deep neural network model and thermodynamic calculations to conduct experiments and determine the anisotropy and crystal growth of troilite. The surface microstructure of troilite was transformed by the thermal reaction in the vacuum on the lunar surface. Similar structures have been found in near-Earth objects (NEOs), indicating that small bodies underwent the same impact-induced thermal events. Thus, thermal reactions in a vacuum are likely ubiquitous in the solar system and critical for space weathering alterations of the soil of airless bodies.