The microstructure of room-temperature silver selenide thin films prepared by pulsed laser deposition (PLD) was investigated by transmission electron microscope (TEM). Two phases existed in room-temperature silver selenide. One was orthorhombic phase (O) and the other was identified as monoclinic phase (M) by TEM tilting experiments. The monoclinic phase can transform to orthorhombic phase along M direction under the irradiation of electron beam. Thermal stress induced by the difference of coefficient of thermal expansion (CTE) of Ag2Se and Cu gridding/NaCl substrate is thought to play an important role in this phase transformation.