The construction of junction sections of long tunnels is the key points of the tunnel construction. There are many junction section construction methods. The features of the junction section construction methods adopted in the construction of Muzhailing tunnel, Tongzhai tunnel and Taoshuping tunnel on LanzhouChongqing railway are presented, compared and analyzed, so as to achieve safe, economic and rational junction section construction methods. It is concluded that the risks, geological conditions and project features should be considered in the selection of the junction section construction methods and that attention should be paid to the construction procedure transition, construction organization and key technologies.