The network operation of the subway can reduce the number of passenger transfers and improve subway operation efficiency. Based on the subway smart card data, this paper proposes an optimal design method for the cross-line operation scheme of subway trains. The method firstly calculates the OD matrix between subway stations, the passenger section flow, and the transfer flow according to the passenger smart card data. It then optimizes the design of the subway train cross-line operation plan, including determining the routing type of cross-line operation and the number of trains running. Finally, for the lines with cross-line operation conditions in the urban subway system, we design the cross-line operation schemes under all possible combinations. According to the volume of the cross-line passenger flow that the cross-line trains can carry, the top-ranked operation plans are preferably recommended. Taking the Chengdu subway network as an example, the research results show that, in the Chengdu subway network, the North Railway Station, Xibo City Station, and South Railway Station bear the highest transfer demand. The transfer demands that can be undertaken by cross-line trains are 23,934, 16,710, and 13,024 trips per hour, respectively. This shows that the proposed design method can accurately and reasonably screen out the transfer stations and lines with an urgent need for cross-line trains.