Morphological change of amorphous ice films of D2O has been studied through adsorption of methane using thermal desorption spectroscopy (TDS) and infrared reflection absorption spectroscopy under ultrahigh vacuum. The investigated ice films were prepared under several different conditions; first, water (D2O) molecules are evaporated onto a Ru substrate at 25 K, and then subjected to an annealing process at various temperatures prior to methane deposition. On ice annealed at low temperatures, two desorption species of methane were observed in TDS: one was derived from methane adsorbed near the ice surface and the other was attributed to the desorption of methane encapsulated in ice during heating. Only the former species was observed when the annealing temperature exceeded 60 K. This indicates that reconstruction of ice occurs below 60 K, which inhibits the encapsulation of methane molecules from the amorphous ice. On the other hand, infrared spectra of ice covered with methane show that the micropores in ice start to collapse at similar to80 K, and ice becomes pore free at 120 K. We have found that the morphological change of amorphous ice induced by thermal relaxation takes place in a stepwise manner.