One of the most encountered obstacles for utilizing nano-sized vehicles to implement the in vivo delivery of nucleic acid drugs (NADs) is the possible steric hindrance caused by their intrinsic size and charge. In this work, we added Ca2+ for the pH triggered self-assembly process of H-apoferritin (HFn), to neutralize negative charges and help siRNA condense during complexation and particle formation. As expected, the internalization efficiency of siRNA in HFn particle formation could be enhanced 1.65-fold, compared with that without incorporated Ca2+. Furthermore, the calcification that occurred within the cavity of HFn particles endows them with endosomal escape capability, which could explain their contribution to the demonstrated in vitro and in vivo gene silencing effect achieved by the internalized siRNA. Thus, this Ca2+ participating self-assembly process of a protein nanostructure would lead to advanced internalization efficiency for NAD therapy.