The microstructure plays a crucial role in the manufacturing and application of polyacrylonitrile fibers, which serve as precursors for carbon fibers. Synchrotron radiation small angle x-ray scattering (SR-SAXS) is a non-destructive and precise technique for analyzing fiber structures. This study employed one-dimensional SR-SAXS mapping to extract key structural parameters such as periodicity, lamellae thickness, and the extent of amorphous regions, as well as the directional orientation in γ-irradiated, pre-oxidized polyacrylonitrile fibers. The analysis revealed a three-layered structure comprising a surface skin, a transitional layer, and a central core. Notably, the lamellar thickness exhibits a “U”-shaped distribution, while the long-period structures, amorphous regions, and orientational properties demonstrate a “wave-like” pattern. Within this structure, the skin exhibits a higher level of orientation, with the orientation decreasing progressively from the skin toward the core layer. The structure of the layered crystal was further corroborated by the morphological analysis. In addition, molecular simulations were performed to propose the mechanisms underlying the formation of this layered structure. This comprehensive investigation using SR-SAXS and one-dimensional mapping provides detailed insights into the microstructural and morphological characteristics of polyacrylonitrile fibers, which can inform future advancements in material processing and refinement techniques for the production of advanced fibers.