The functional group distribution and skin–core structure of polyacrylonitrile (PAN) pre-oxidized fibers have been evaluated by solid-state 13C-NMR, electron probe micro-analysis, element analysis, nano-infrared spectroscopy atomic force microscopy, and optical microscopy. The pre-oxidized fibers exhibited a skin–core structure with high optical density (OD) values in the skin and low OD values in the core. As the heat treatment temperature was increased, the OD of the pre-oxidized fibers increased, which is because of the formation of C = O, C = N, C = C, and their conjugated structures of C = N with C = C. The difference in the OD values between the pre-oxidized fiber skin and core became increasingly apparent as the heat treatment temperature increased, with the OD difference increasing from 0.045 at 220 °C to 0.085 at 260 °C. The OD difference is closely related to the oxygen element and C = O functional groups in the fiber. The contents of the oxygen element and C = O in the pre-oxidized fiber skin were higher than those in the pre-oxidized fiber core. At a heat treatment temperature of 260 °C, the relative content of C = O in the skin was 0.454, whereas that in the core was 0.313, which was consistent with the trend of the OD value change. In comparison, C = C and C = N formed during pre-oxidation were not substantially distributed in the radial direction of the fibers. The radial inhomogeneity of the pre-oxidized fiber was mainly affected by the radial difference of the carbonyl content.