The issuance of “all-in-one response code for boarding public transport vehicles” and “all-in-one response code for Changxing (Unimpeded) transportation in Chongqing” by Chongqing Payeasy and Chongqing Rail Transit Group has enabled boarding codes to be provided by two app platforms. At the same time, a variety of new mobile payment channels, for example, UnionPay, Alipay, and WeChat, has been introduced, which necessitates improvement of the reader function of the automated fare collection (AFC) system. The software and hardware of the whole network system of the existing operational lines are redesigned to achieve synchronous application of the multiple mobile payment channels in an efficient, convenient, and safe way and toovercome the difficulties facing riders and rail group operators. Considering the current status of the rail transit AFC system, improving the mobile payment system is complicated and hard task with a tight schedule, which involves a wide range of things, including multiple interfaces, etc.. This study details the strategic measures for the selection of rail transit mobile payment media, mobile payment system design, and mobile payment system improvement and implementation, providing a better solution for implementation of a multicode platform and multiservices.