Existing traveling wave fault line selection methods for a small current grounding system highly rely on the initial head of the traveling wave. To help overcome this deficiency, this paper proposes a fault line selection method based on the comparison of comprehensive similarity of traveling wave current waveforms for a small current grounding system by analyzing the refraction and reflection process of the fault traveling wave in three-core cable. First, it extracts the time-frequency information of the traveling wave current caused by cable faults in metal sheath grounding wire by S-transform, then constructs the time-frequency energy matrix and waveform similarity matrix of the traveling wave current signal. It then calculates the comprehensive similarity coefficient of traveling wave shape of each line with other lines according to the waveform similarity matrix. Finally, it accomplishes the fault line selection by comparing the comprehensive similarity coefficient. Simulation and measured data analysis shows that the proposed method can make full use of the transient traveling wave fault information, and is not affected by the neutral point grounding mode, fault location and transition resistance of the system, and the line selection results are accurate and reliable. This work is supported by the National Key Research and Development Program of China (No. 2017YFB0902800).