We have investigated a post-annealing effect on microscopic structural changes of kink boundaries (KBs), which have been initially introduced by a hot-extrusion of an Mg-Zn-Y alloy containing long period stacking/order (LPSO) phase, based on scanning transmission electron microscopy (STEM) and atom-probe tomography (APT). STEM observations show that most of the KBs appear to be segmented into several submicron-scale, each of which is composed of arrays of extended basal (a-) dislocations that are geometrically necessary to account for the LPSO crystalline rotations. Atomic-scale STEM/APT observations reveal significant reconstructions of these extended dislocation-core structures, which occur at the solute-enriched face-centered cubic layers in the LPSO structures and forms local hexagonal close-packed Mg region with distinct solute depletions. These recovery-like features indeed enhance the thermal stability of the KBs, and the corresponding driving force can be reasonably described according to disclinations, whose elastic energy is defined by crystal rotations and the relevant dipole distances.