Sub-nanometric particles (SNPs) of atomic cluster sizes have shown great promise in many fields such as full atom-to-atom utilization, but their precise production and stabilization at high mass loadings remain a great challenge. As a solution to overcome this challenge, a strategy allowing synthesis and preservation of SNPs at high mass loadings within multishell hollow metal-organic frameworks (MOFs) is demonstrated. First, alternating water-decomposable and water-stable MOFs are stacked in succession to build multilayer MOFs. Next, using controlled hydrogen bonding affinity, isolated water molecules are selectively sieved through the hydrophobic nanocages of water-stable MOFs and transferred one by one to water-decomposable MOFs. The transmission of water molecules via controlled hydrogen bonding affinity through the water-stable MOF layers is a key step to realize SNPs from various types of alternating water-decomposable and water-stable layers. This process transforms multilayer MOFs into SNP-embedded multishell hollow MOFs. Additionally, the multishell stabilizes SNPs by pi-backbonding allowing high conductivity to be achieved via the hopping mechanism, and hollow interspaces minimize transport resistance. These features, as demonstrated using SNP-embedded multishell hollow MOFs with up to five shells, lead to high electrochemical performances including high volumetric capacities and low overpotentials in Li-O-2 batteries.