Power flow controllers (PFCs), which adopt high voltage and large power converters, are the significant device of cophase traction power supply systems (TPSSs); therefore, it is important to enhance the reliability of PFCs. Due to the limited capacity of power semiconductor switches, parallel connection of PFC units has been encouraged, and system reliability can be enhanced by configuring standby PFC units. However, while the increase in the number of redundant modules is accompanied by higher investment, the reliability improvement also has a saturation effect. In addition, among the control techniques of parallel PFCs, one of the commonly employed methods is current-sharing control, but the thermal stress of converters is increased at low loads. Therefore, in this article, a PFCs’ cost model is built based on life cycle cost (LCC) theory, and the number of basic, redundant PFC units is determined with the constraint of the minimum average annual cost. Furthermore, an improved coordinated control strategy that can alleviate thermal stress is proposed. Under a high load, all the PFC units are operated simultaneously, while, under a low load, the units are operated by turns. Moreover, to ensure consistent reliability and maximize system reliability, the rotation working time of each unit and the load demarcation point are optimized considering negative sequence compensation constraints. Case studies show that the given control strategy can extend the life span up to 26.30% and achieve a 19.11% cost reduction.