Amorphous MoO x (a-MoO x , 2<x<3) thin films were deposited by a reactive magnetron sputtering method. As the Li-ion storage electrodes, the a-MoO x thin films exhibit a high capacity of 338μAh·cm−2 (about 845 mAh·g−1) at a current density of 90μAcm−2 even after 100 electrochemical cycles, and have a rate capacity of 158μAhcm−2 at a high current density of 2000μAcm−2. The phase analysis revealed that all the a-MoO x thin films maintained an amorphous characteristic after having been charged-discharged at various stages. In-situ electron-beam irradiation (EBI) induced crystallization of the a-MoO x thin films was performed by using a transmission electron microscopy. By analyzing the EBI induced crystalline phases of the a-MoO x thin films, the possible electrochemical reactions during the charge-discharge processes were discussed. According to the developed investigation method, the possible electrochemical mechanism in the a-MoO x thin films were proposed to undergo a conversion reaction such as MoO x +2xLi+ +2xe− ↔Mo+ xLi2O during the electrochemical processes.