The invention provides a travelling wave protection method and a lightning stroke interference determining method and device of a flexible DC system. Voltage signal of the flexible DC transmission system are collected, and S transformation is carried out on the voltage signals to obtain a 2D multi-time-frequency matrix; and amplitudes of sampling points in the set frequency band are extracted fromthe 2D multi-time-frequency matrix, the change trend of the amplitudes of the sampling points in the set frequency band is determined, if the amplitude change trend satisfies a set condition, it is determined that a lightning stroke interference occurs in a line of the flexible DC transmission system, and otherwise, it is determined that a fault occurs in the flexible DC transmission system, anda travelling wave protection motion is made. According to the methods and device, the computational complexity is low, less time is consumed, a computing process is simple, the travelling wave fault determining efficiency of the DC transmission system is improved, faults can be removed rapidly, equipment damage caused by fault of the power line can be reduced greatly, impact on the AC grid is reduced, power failure loss of the power grid is reduced, severe power failure accidents due to instability of the primary power grid can be prevented, and the reliability of the DC power grid is improved.