The transformation of functional groups and development of radial structural heterogeneity during the thermal stabilization of polyacrylonitrile (PAN) precursor fibres were quantitatively defined for the first time using high resolution spectroscopic imaging techniques. The infrared imaging of isothermally treated fibre cross-sections reveals the radial distribution of specific functional groups (CN, CN, CH₂, CH and CO) that forms the ladder polymer structure, the most critical stage in the precursor stabilization process. Apparently, it was found that the cyclization reaction of PAN polymer chains occurred at a faster rate in the core of the fibre during heating where it further selectively promoted the dehydrogenation reaction. On the other hand, the conversion of sp³ to sp² hybridized carbon atoms was found to be higher around the skin layer compared to the core of the fibres, thus providing evidence for different cross-linking mechanisms in these regions. The simultaneous occurrence of a higher extent of cyclization and dehydrogenation reactions due to the excess heat developed in the core and a delay of oxygen diffusion in to the core of the fibres played a critical role in the polymer chain cross-linking in the skin and core regions that further led to the evolution of radial heterogeneity in the fibres. It was also found that the mechanical properties were built upon the structural transformations and the variation in the modulus across the fibre cross-section further confirmed the reaction mechanism.