A microwave heating method was used for oxidative stabilization of polyacrylonitrile (PAN) fibers. The bulk density, chemical structure (FTIR), crystalline structure (WAXD), and skin-core structure were studied. The results show that the intermolecular cyclization happened above 220 °C. From X-ray diffractograms of heat treated fibers, the pre-graphitic structure of stabilized fibers was developed to turbostratic structure. A gradual densification of the fibers occurring was observed after stabilization at a maximum temperature of 240 °C. Microwave heating effectively shortened the thermal stabilization process and the thermal stabilization time by 35 min compared with the conventional thermal stabilization process. The skin-core structure of the stabilized fibers was prohibited by microwave heating.