Self-assembly of copper(II)phenylsilsesquioxane assisted by the use of 1,10-phenanthroline (phen) results in isolation of two unusual cage-like compounds: (PhSiO_1,5)₁₂(CuO)₄(NaO_0.5)₄(phen)₄ 1 and (PhSiO_1,5)₆(PhSiO_1,5)₇(HO_0.5)₂(CuO)₅(O_0.25)₂(phen)₃ 2. X-Ray diffraction study revealed extraordinaire molecular architectures of both products. Namely, complex 1 includes single cyclic (PhSiO_1,5)₁₂ silsesquioxane ligand. Four sodium ions of 1 are additionally ligated by 1,10-phenanthrolines. In turn, “sodium-less” complex 2 represents coordination of 1,10-phenanthrolines to copper ions. Two silsesquioxane ligands of 2 are: (i) noncondensed cubane of a rare Si₆-type and (ii) unprecedented Si₇-based ligand including two HOSiO_1.5 fragments. These silanol units were formed due to removal of phenyl groups from silicon atoms, observed in mild conditions. The presence of phenanthroline ligands in products 1 and 2 favored the π–π stacking interactions between neighboring cages. Noticeable that in the case of 1 all four phenanthrolines participated in such supramolecular organization, unlike to complex 2 where one of the three phenanthrolines is not “supramolecularly active”. Complexes 1 and 2 were found to be very efficient precatalysts in oxidations with hydroperoxides. A new method for the determination of the participation of hydroxyl radicals has been developed.