Sodium borosilicate (NBS) glass is one of the candidate materials for high-level waste glass immobilization. A large number of experiments are performed to study the effect of irradiation by electrons or heavy ions on this type of glass. However, only a few researches of numerically investigating the effect of irradiated NBS glass have been reported. Furthermore those studies mainly focus on heavy-ion irradiation, and none of them is devoted to simulating the effects of electron irradiation on glass that has been irradiated by electrons, especially for structure evolution. In this paper, we propose a novel method of using molecular dynamics (MD) to simulate structure evolution of electron-irradiated NBS glass with compositions of 67.73% SiO2, 18.04% B2O3 and 14.23% Na2O, in mol.%. This method is based on the previous experimental results of Raman spectra and mechanism of structure transformation in irradiated glass. The Raman spectra confirm that the peak indicating the existence of molecular oxygen appears at 1550 cm-1 in irradiated glass. It is assumed that those oxygen atoms do not have any interactions with other adjacent atoms nor participate in the glass network recombination. This assumption is reasonable, for molecular oxygen mainly exists as dissolved oxygen instead of oxygen bubble and is located at interstice of glass network. Thus the presence of molecular oxygen does not have any effect on glass network structure. Then irradiated glass can be obtained by gradually randomly removing a certain number of oxygen atoms from the pristine glass. The glass with removed oxygen atoms is regarded as an irradiated glass which is considered as one irradiated by electrons in experiments. The results derived from MD simulation include average SiOSi bond angle, ring size distribution, sodium profile, evolution of [BO4] units, and [BO3] units. With the increase of removed oxygen atoms, the average bond angle of SiOSi decreases and the number of small rings gradually increases in irradiated glass. Besides, sodium phase separation is observed obviously after extensively removing oxygen. Moreover, in the process of removing oxygen, some [BO4] units transform into [BO3] units, and the transformation process reaches a saturation state finally. Those effects derived from MD such as decrease of SiOSi bond angle, increase of small rings in number, phase separation of sodium and structure change between [BO4] units and [BO3] units, are consistent with those of glass irradiated by electrons in previous experiments. Therefore, the method proposed in this paper will provide a new perspective to understand the mechanism of structure evolution in sodium borosilicate glass after being irradiated by electrons.