Metro is being developed rapidly in second-tier cities. There is a need to understand the impact it brings as it relates to the planning and management of the whole urban transportation system. In this paper, we applied the multilayer complex network theory to study this problem by contrasting the characteristics of transportation networks before and after the metro is built. We focused on transportation networks in second-tier cities and (1) proposed edge functions of the road subnetwork and rail transit subnetwork with impedance as weight; (2) established an interlayer function based on the transfer behavior to couple the above subnetworks into the multilayer weighted transportation network; and (3) redefined statistical parameters, such as node strength, chessboard coefficient, and average least pass cost. At last, Hohhot, China, a typical second-tier city, was taken as a case study. Calculations show that the new-built metro network in the second-tier city increases convenience and reduces travel cost, whereas, the vulnerability of the whole network increases, and the distribution of key nodes in the road network is reconstructed. For the sustainable development of urban transportation, more attention should be paid to the new-built metro in second-tier cities.