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Smoothing reactors, together with the DC filter banks installed at both ends of the HVDC transmission line constitute the `natural boundary', which leads to significant difference in attenuation characteristic of different frequency components of fault transient signals detected by protection. By means of Hilbert-Huang Transform, which is a kind of non-stationary transient signal processing method, the energy of high frequency components(2000Hz~10kHz) is extracted based on the attenuation characteristic of the line boundary, then a novel algorithm for the non-unit transient-based protection is acquired. Moreover, a protection threshold that is adapt to various lengths of transmission line is obtained by extensive simulation work. Experimental results indicate that the new criteria can identify any internal fault on the whole line and clear it rapidly and credibly, what's more important, the accuracy and reliability of the criteria will not be influenced by the length of the transmission line.