With the current popularity of Electric Vehicles (EV), especially in some critical EV applications such as hospital EV fleets, the demand for continuous and reliable power supply is increasing. However, most of the charging stations are powered in a centralized way, which causes transistors and other components to be subjected to high voltage and current stresses that reduce reliability, and a single point of failure can cause the entire system to fail. Therefore, a significant effort is made in this paper to improve the reliability of the charging system. In terms of charging system structure design, a distributed charging structure with fault tolerance is designed and a mathematical model to evaluate the reliability of the structure is proposed. In terms of control, a current sharing control algorithm is designed that can achieve fault tolerance. To further improve the reliability of the system, a thermal sharing control method based on current sharing technology is also designed. This method can improve the reliability of the charging system by distributing the load more rationally according to the differences in component performance and operating environment; FPGA-based control techniques are provided, and innovative ideas of pipeline control and details of mathematical reasoning for key IP cores are presented. Experiments show that N + 1 redundancy fault tolerance can be achieved in both current sharing and thermal sharing modes. In the current sharing experiment, when module 3 failed, the total current only fluctuated 800 mA within 500 ms, which is satisfactory. In the thermal sharing experiment, after module 3 failed, modules 1, 2, and 4 adjusted the current reasonably under the correction of the thermal sharing loop, and the total current remained stable throughout the process. The experimental results prove that the charging system structure design and control method proposed in this paper are feasible and excellent.