The widely used flywheel energy storage (FES) system has such advantages as high power density, no environment pollution, a long service life, a wide operating temperature range, and unlimited charging–discharging times. The flywheel array energy storage system (FAESS), which includes the multiple standardized flywheel energy storage unit (FESU), is an effective solution for obtaining large capacity and high-power energy storage. In this paper, the strategy for coordinating and controlling the charging–discharging of the FAESS is studied in depth. Firstly, a deep analysis is conducted on the loss generated during the charging–discharging process of the FESU. The results indicate that the loss is related to the charging–discharging of power. To solve the problems of over-charging, over-discharging, and overcurrent caused by traditional charging–discharging control strategies, this paper proposes a charging–discharging coordination control strategy based on the equal incremental principle (EIP). This strategy aims to minimize the total loss and establish a mathematical model of optimal coordination control with the constraints of total charging–discharging power, rated power limit, over-charging, over-discharging, and overcurrent. Based on the EIP, the optimal distribution scheme of power charging–discharging is determined. Secondly, this paper gives the specific implementation scheme of the optimal coordinated control strategy. Lastly, the charging–discharging coordinated control strategy is verified by examples. The results show that the coordinated control strategy can effectively reduce the loss during the charging–discharging process and can prevent over-charging, over-discharging, and overcurrent of the system. Overall, it has a better control effect than the existing charging–discharging control strategies.