A fault location method based on natural frequencies can work accurately without identifying the wave front. The key factor of this approach is to correctly extract principal component of the natural frequencies of fault travelling wave. Considering the discontinuous wave impedance， the natural frequencies spectra of mixed overhead-cable lines may be aliased and cause difficulties in identifying and extracting the principal component of natural frequencies. In order to handle this more effectively， a fault location method based on natural frequencies and empirical mode decomposition（EMD） for mixed overhead-cable lines is proposed. By using EMD， a signal can be decomposed to obtain the required part of the travelling wave before extracting the principal component of natural frequencies spectra of travelling wave. The natural frequencies spectra can be analysed subsequently to extract the principal component of natural frequencies spectra of the faulty travelling wave to finally obtain the fault location（s）. Simulation on a 110 kV mixed overhead-cable line system shows that the proposed method can satisfactorily solve the spectra aliasing problem in fault location studies for mixed overhead-cable lines in frequencies domain. It has potential values for practical usage.