The mechanism of self-assembly induced by H2O molecules is studied for layered saponite nanoparticles and zeolite with the cage structure by means of positronium (Ps) annihilation spectroscopy together with thermogravimetry and differential thermal analysis (TG-DTA). Prior to hydration the saponite exhibits two kinds of open spaces with their sizes of ∼3 Å and ∼9 Å, whereas open spaces with their sizes of ∼3 Å and ∼5 Å corresponding to β and α cages are obtained for the zeolite. The occupation of both α and β cages by H2O molecules proceeds along with hydration up to 2.5 h, which well synchronizes with the weight gain in TG data. On the contrary, the angstrom-scale open spaces for the saponite vary with hydration in the time scale with ∼100 h much longer than that of TG-DTA with ∼8 h. The present results suggest that the long-term self assembly originates from not the cage but the nanolayered structures.