An intelligent comparison method for fault waveform data is proposed based on the fast dynamic time warping (FDTW) algorithm to address the problem of the lack of channel identification information in fault recorder wave files of intelligent substation protection devices. This lack makes it difficult to correspond with the fault recorder wave files of the same source channel. First, anomaly detection is performed on the fault waveform data extracted from each substation to ensure the quality of the data in the fault waveform files. Second, the Lagrange interpolation method is used for sampling frequency conversion to deal with inconsistent sampling frequencies between the protection device and the fault waveform recorder. Then, the Euclidean distance is used to align the waveform consistency of the same source waveform files to achieve clock synchronization. Finally, the FDTW algorithm is used to intelligently compare the fault waveform data without channel identification information. Case studies show that the proposed method can process the fault waveform data into a consistent type, quickly and accurately calculate the similarity of waveforms to be matched, achieve the matching of the fault waveform data from the same source channel, and has strong stability and real-time performance.