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This paper proposes a novel transmission line protection scheme based on frequency-domain model identification method with distributed parameter. Integrated impedance is defined by voltages and currents of two end terminals of transmission line. By analyzing the frequency-domain expressions of integrated impedance in internal and external fault states, the amplitude-frequency characteristics of the integrated impedance are discussed. The integrated impedance in internal fault state shows system impedance characteristic and the integrated impedance in external fault state shows the line distributed capacitive characteristic. The frequency-domain model errors are defined as unbalanced currents respectively in order to identify the internal and external faults. Matrix pencil algorithm is used to calculate the phasors in different frequencies in the proposed scheme. Protection criterions are designed and some tests are performed. The simulation results show that the proposed schemes can detect internal fault quickly and reliably. Furthermore, the influences from capacitive currents and transition resistances can be avoided in the proposed protection scheme.