Compared with the homogeneous transmission lines, the hybrid ones are composed of the overhead, underground and submarine cable lines, resulting in three different sets of parameters over the transmission path and posing great challenge to fault location. This paper proposes a fault section identification method for two types of the hybrid lines based on modal-domain analysis which eliminates the effects of the refractions and reflections at the cross-bonded nodes. First, a method for decoupling the transients in the high-voltage cable is proposed to obtain the unified model of two types of the hybrid lines in modal domain. Then, the concept of the energy of the decoupled transient is defined, the reflection and refraction features of the energy of the transient signal are analyzed, and a novel fault section identification method is developed based on the transient energy ratio. Finally, the model of a 110kV hybrid transmission line is established in PSCAD/EMTDC. Various fault experiments are conducted. The results show the effectiveness of the proposed method.