The speed requirement for the main protection of the MMC-HVDC system is extremely high. The introduction of a large number of high-frequency transient signals after the line is disturbed by lightning strikes can easily lead to misoperation of line protection. To solve this problem, this paper first analyzes the characteristics of a line voltage traveling wave after lightning strike according to the propagation law of traveling waves. The characteristic difference between lightning disturbance and fault is obtained. When lightning disturbance occurs, the polarity of the wave head does not change after the voltage traveling waves is reflected by the line boundary during the transient process, and the time interval between the traveling waves head and the line boundary is large; when the lightning fault occurs, the polarity of the voltage traveling waves changes after being reflected by the fault point, and the time interval between the traveling waves head and the line boundary is small. Then, based on voltage traveling waveform features, a lightning interference identification method combining long and short windows is proposed. Finally, the proposed method is validated using PSCAD/EMTDC electromagnetic transient simulation software. The results show that the proposed lightning interference identification scheme can quickly, reliably, and accurately identify lightning interference and fault conditions, independent of the location of lightning strikes, line parameters, lightning current parameters, and noises.