Traditional double-terminal travelling wave protection schemes are unable to satisfy the requirement of power systems stability and economy. In order to solve these problems for extra high voltage (EHV) transmission lines protection, a novel non-unit transient protection based on HHT energy spectrum is developed. The travelling-wave characteristics between internal faults and external faults are analysed. The main difference is that the travelling wave high frequency components energy caused by the internal faults is larger than that caused by the external faults due to the influences of line trap and bus-to-ground capacitance. Intrinsic mode functions (IMF) of travelling wave are extracted by the empirical mode decomposition (EMD). And then Hilbert-Huang transform (HHT) is utilised to calculate the corresponding instantaneous frequency of each IMF component to obtain energy spectrum. Finally, the energy spectrum is applied to distinguish the internal and external fault. EMTP simulation results show that, under different fault conditions, the novel scheme can distinguish reliably the internal faults from external faults and protect the whole transmission line with high sensitivity.