The flexible excitation system (FES) is a kind of novel excitation system with two channels for damping control. Besides the basic functions of traditional excitation systems, flexible excitation systems can provide reactive power support for the terminal voltage, and the large-capacity FES can improve the voltage stability and power-angle stability of synchronous generator units. However, with the increase in system capacity and the complication of control objectives, the difficulty of controller design will be increased. The randomness and fluctuation of new energy resources such as photovoltaic and wind turbines may cause disturbance and fault to the power system, which requires the coordinated control strategy for the FES to achieve stability in voltage and power angle. In this paper, the basic characteristics of FES are analyzed, and the mathematic model of the single machine infinite bus (SMIB) system based on FES is derived. The coordinated control strategy based on decoupling control of stator and rotor is proposed according to the optimal objectives of voltage stability and power-angle stability, and the linear optimal excitation control (LOEC) is adopted with the adaptive amplitude limiter (AAL) determined by fuzzy rules. The MATLAB/Simulink platform is established and the results verify the superiority of the proposed LOEC + AAL control strategy in large disturbance working conditions, which showed better robustness. The proposed coordinated control strategy provides an effective solution for industrial application and performance improvement of FES.