The existing methods of hydrogen storage bottlenecked advancements in its commercialization on an industrial scale. Here, the hydrogen storage capacity via the hydrogen clathrate hydrate in ice Ih (HCHinIh) with the aid of nanobubbles is further improved to 3.442–3.494wt% from the previous 3.441wt%. These nanobubbles are designedly arranged within 0.5 mm diameter individual ice spheres which initially pack in simple cubic form, and then used to synthesize the hydrogen clathrate hydrate as does HCHinIh. The total volume of nanobubbles is adjustable by deploying their different space layouts. In addition, we propose that the bubble formation is driven by transforming the pre-melted quasi-liquid layer (PMQLL) to solid ice-like in an ice-like nanotube, which is a structure comprised of PMQLL and ice surrounding PMQLL (PMQLL-ice) analogous to a carbon nanotube-graphene sheet (CNT-GS) structure, where the interaction energy related to O-O and O-H in PMQLL-ice is 0.08–6.17 times that of C-O and C-H in the CNT-GS structure.