The development and construction of thrust faults in mountain front areas are quite complicated, causing interpretation difficulties with electrical resistivity. To address these difficulties, an optimal stratification method involving magnetotellurics (MT) was applied, based on Fisher's clustering method for continuous data. The feasibility and effectiveness of this method are verified by applying it to the MT exploration data in Qiangtang Basin, Qinghai-Tibet Plateau, China. The results show that the optimal stratification method can improve the resolution of the resistivity model effectively in areas with complex structures. The MT inversion section after optimal stratification reflects the stratum interface, fault and structure style more directly and can be used for comparison with seismic data. The Fisher segmentation method can be applied to the interpretation of the MT data as a supplementary method, especially in the complicated structural belts, areas in which the geological structure and deformation information cannot be recognized effectively by conventional methods.