This research aims to investigate the influence of 3D through-thickness stitching on the gas permeability and transverse microcracking of cryogenically cycled carbon/epoxy composites. 3D through-thickness stitching can be used to improve the interlaminar properties of polymer matrix composites (PMCs) and produce lightweight, unitized structures for cryogenic storage tanks. To fully utilize stitched composite structures for these applications, their inherent gas permeability challenges must be understood. Therefore, in this study, the stitched composites' damage evolution and gas permeability was experimentally characterized under a) pure thermal stress, b) thermal and uniaxial mechanical stress, and c) thermal and biaxial mechanical stress. Helium gas permeability was measured for each specimen at room or cryogenic temperatures under a mechanically strained state following the thermo-mechanical cycles. Optical microscopy was used to measure microcrack densities and monitor their evolution through the thickness of the composite specimens. Thin plies, graphene nanoplatelets (GNP) modified resin, and a hybrid barrier layer comprising of both were incorporated in the stitched specimens as barrier layers to reduce their gas permeability. The dependence of gas permeability of stitched composites on the mechanical strain, test temperature, and load history was evaluated and correlated to microcrack density. A significant reduction in permeability and damage evolution (transverse microcracks and delaminations) was obtained for all thermo-mechanical cases using the hybrid barrier layer laminate. Additionally, the permeability was several orders of magnitude lower than the allowable. Overall, the hybrid barrier layer shows tremendous promise as a viable barrier layer for stitched/unstitched composites undergoing thermo-mechanical fatigue involving a cryogenic environment.