Lightning interference can easily cause maloperation of traditional flexible DC transmission line protection. Therefore, it is crucial to quickly and accurately distinguish lightning interference from faults after protection is activated. This paper analyzes the theoretical expressions of the line-mode voltage traveling wave under different disturbances, and examines the time-frequency transformation mechanism using the S-transform. It is finds that, in the case of lightning interference, the instantaneous amplitude-frequency curve exhibits only one peak; in the case of a fault, the instantaneous amplitude-frequency curve has multiple peaks. Additionally, there is a significant difference in the main frequency magnitude in lightning faults and regular short-circuit faults. Based on these characteristic differences, a complete method for identifying lightning disturbances is proposed. The simulation results based on PSCAD/EMTDC show that the proposed method quickly and reliably distinguish lightning interference form lightning faults and short-circuit faults.