Fully-coupled thermo-mechanical simulations are implemented in COMSOL Multiphysics to investigate micro-scale stress-strain variability in pegmatite specimens subjected to thermal loading using microwaves. Thermally-induced compressive and tensile stresses increase as the microwave irradiation duration increases. The dielectric constant, coefficient of expansion, and type and size of mineralogical boundary have significant impacts on the responses of the rock to microwave irradiation. The maximum principal stress of the chlorite is the smallest, indicating that the chlorite experiences the most damage under microwave irradiation, followed by the quartz. The maximum principal stress values of plagioclase and orthoclase are larger, indicating that they are likely to incur the least damage. Where quartz or chlorite is dominant, the resulting von Mises stresses are consistently higher after 120 s of microwave irradiation. The rate of generation of von Mises stresses increases most rapidly along the interface between quartz and plagioclase, and the interface between quartz and orthoclase, followed by the interface between quartz and chlorite, and finally the interface between plagioclase and orthoclase. The presented modeling approach provides a practical method to investigate stress-strain relationships within mineralogical boundaries inside a rock thin section.