Based on the analysis of the factors that affect system nature frequencies， a protection scheme based on nature frequencies is proposed. It is analyzed that the nature frequencies exist in fault component besides power frequency and the energy is strong and easy to sample. For phase-to-phase faults， the differences of nature frequencies at two ends of transmission lines and the impedance criterion are used to identify internal and external faults. Compared to conventional protection schemes， this scheme can decrease action time for internal fault. The scheme is immune to system oscillations， load current， fault time， transient resistance， fault location and mode of operation. Moreover， the current transformer saturation has less influence on the scheme. ATP simulation and MATLAB analysis verify the effectiveness of the scheme.