The invention discloses an integrated highly-reliable magnetic suspension energy storage flywheel digital control device, which is a device capable of controlling a magnetic suspension energy storage flywheel system motor and an electromagnetic bearing, and comprises an interface circuit, a field programmable gate array (FPGA) system, a magnetic bearing control power module, a motor control powermodule, a magnetic suspension energy storage flywheel system, and a sensor circuit, wherein the FPGA system acquires a magnetic bearing rotor displacement signal, a rotation speed signal, a magnetic bearing coil current, a motor winding current, and the like through the interface circuit. On one hand, the FPGA system performs active control on the electromagnetic bearing according to the magneticbearing rotor displacement signal, the magnetic bearing coil current and the rotation speed signal; on the other hand, the FPGA system controls the rotation speed of the flywheel according to a rotation speed instruction, the motor winding current and the rotation speed signal. By the invention, integrated design of a magnetic bearing digital controller and a motor digital controller is realized,the integration level and reliability of magnetic suspension energy storage flywheel system controller is improved, the volume and weight are reduced, and the power consumption of the controller is lowered.