Polycrystalline silicon carbide (SiC) has been significantly used as a susceptor material during microwave-based material processing owing to its excellent microwave absorption properties. However, the interaction of microwaves with polycrystalline SiC at an atomic level has not been explored experimentally or theoretically. This work investigates the microwave heating characteristics of polycrystalline cubic 3C-SiC through molecular dynamics (MD) simulation using the Vashishta interatomic potential. The effect of change in electric field strength and frequency on the structural evolution and thermo-physical properties of polycrystalline 3C-SiC has been studied. The study revealed that the presence of grain boundaries in polycrystalline 3C-SiC structures plays a critical role in enhancing microwave absorption efficiency. Microwave exposure to polycrystalline 3C-SiC beyond 2830 K significantly increases total energy; consequently, a solid-to-liquid transition occurs in the 3C-SiC structure, initiated from the grain boundaries. Further, an increase in microwave exposure time results in a reduction in grain size due to rapid microwave absorption at grain boundaries. The phase transition temperature of polycrystalline 3C-SiC was observed to be 14% lower than that of the single-crystal 3C-SiC.