It was found that BST thin film was damaged by the irradiation of high density electron beam (the current density was about 2 nA/cm2). In-situ and real time EELS showed that the intensity ratio of Ti to O edge and the distance between Ti and O edge changed. It indicated that the film lost oxygen and thus the oxidation states of positive ions lowered. EELS study with high spatial resolution proved that compared with the inner of columnar grains, the grain boundaries with special structure and chemical environment were the main passageway of oxygen loss.