In this study, how physical differences in the microstructure of additively manufactured (AM) pure Ni affect its susceptibility to hydrogen embrittlement (HE) are investigated. The presence of high-density dislocation cells (DCs) and grain boundaries in AM Ni could absorb more hydrogen therein, with the DC boundaries serving as reversible hydrogen trapping sites. The DC boundaries overlapped with the grain boundaries might lead to an enhanced hydrogen diffusion therein for AM Ni. Consequently, an increased depth of hydrogen-affected region and accelerated failure process were observed in AM Ni during tensile testing due to intergranular cracking. Furthermore, the HE resistance can be slightly improved by a dislocation-cell elimination heat treatment for AM Ni-800, but it remains lower than that of traditionally manufactured Ni, primarily due to the residue of bi-modal grains with small grains along the molten pool boundaries. The underlying HE mechanism based on the structural heterogeneities at different scales for pure Ni is discussed.