Self-assembly of copper(II)phenylsilsesquioxane assisted by the use of 1,10-phenanthroline (phen) results in isolation of two unusual cage-like compounds: (PhSiO1,5)12(CuO)4(NaO0.5)4(phen)4 1 and (PhSiO1,5)6(PhSiO1,5)7(HO0.5)2(CuO)5(O0.25)2(phen)3 2. X-Ray diffraction study revealed extraordinaire molecular architectures of both products. Namely, complex 1 includes single cyclic (PhSiO1,5)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 HOSiO1.5 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.