Structural inhomogeneity of stabilized polyacrylonitrile (PAN) fibers was systematically investigated. When the temperature was not high enough (below 200 °C in an air atmosphere) to initiate either cyclization or oxidation, absorbed oxygen related functional groups on the surface of PAN fibers were observed. However, when the temperature was above 200 °C, oxygen started to penetrate into PAN fibers through the skin, resulting in an increase in the oxygen content and significant relaxation of molecular structure. As expected, oxygen was diffused from the skin to the core with increasing temperature. At 240 °C, Raman spectroscopy confirmed that cyclization homogeneously occurred in the whole cross-section of fibers. However, higher temperature (≥260 °C) resulted in different ratios of D and G bands depending on both position and temperature, indicating that inhomogeneous structures were obtained due to temperature gradient by exothermic reactions. In addition, oxygen level in the core was much less than that on the surface. This provides evidence that there is a limit to equalize oxygen content across the fiber. Therefore, cyclization, dehydrogenation, and oxidation as critical reactions in the stabilization of PAN fibers started simultaneously. Above a certain temperature, in particular, increased activation energy due to oxidation at the surface can cause significant inhomogeneity of the resulting fibers. Display omitted