Graphite cores in nuclear reactors are critical components subjected to severe irradiation conditions. Despite the known susceptibility of graphite to radiation-induced damage, detailed microstructural analyses are limited. Existing works of literature have identified changes in crystallite morphology and orientation as early indicators of structural degradation, but the precise micro-mechanisms are not fully understood. This research explicates these micro-mechanisms using advanced analytical transmission electron microscopy (TEM) to examine irradiated graphite at doses up to 1 dpa (displacements per atom). TEM imaging and diffraction analysis captured detailed changes in crystallite structure. Even at low radiation doses (~ 0.1 dpa), a 15% alteration in crystallite morphology and orientation was observed. Significant crystal lattice rotations up to 5 degrees and micro-deformations were also detected. Additionally, the formation of micro-kinks and kink bands, ranging from 50 to 200 nm, were identified as potential deformation processes, consistent with phenomena in other layered materials. These results advance our understanding of the micro-mechanisms driving structural degradation and deformation in irradiated graphite. This research has significant implications for developing improved models and strategies to enhance the performance and longevity of graphite cores in nuclear reactors, contributing to the advancement of nuclear energy technology.