This paper analyzes the influence of the attenuation of long transmission line to high frequency signal on the principle of line boundary protection. Based on the study of boundary frequency characteristics and the suppression of flat wave reactor to the change rate of current, a new method of line protection is proposed, which is composed of single-ended characteristic harmonic current. In the proposed protection method, by using the amplitude of characteristic harmonic current to construct the start criterion and using the variation of characteristic harmonic current as a protection criterion, the algorithm is simple and transient characteristics of line boundary are fully used. A bipolar 24-pulsating HVDC system model is established in PSCAD/EMTDC. The simulation results show that the criterion can accurately distinguish the fault inside and outside the line and realize the fault pole selection, which is less affected by the transition resistance and long line, and can protect the whole line rapidly. This work is supported by National Key Research and Development Program of China (No. 2017YFB0902600) and National Natural Science Foundation of China (No. 51377068).