This paper proposed a ratio consensus control method based on the Hamiltonian energy theory. By adjusting the rotation speed of flywheel energy storage unit, the ratio consensus control of the system was achieved, and the internal power of the flywheel energy storage system (FESS) is reasonably distributed. First, the portcontrolled Hamilton (PCH) model of the flywheel energy storage unit was established, and the portcontrolled Hamiltonian model with dissipation (PCH-D) was obtained by using the feedback stabilization principle of the PCH system. Then, the problem of ratio consensus control of the flywheel energy storage system was investigated. The speed regulation of the flywheel energy storage unit was realized by using the Hamilton energy forming control strategy to ensure that all the flywheel energy storage units could store and release energy under the same ratio and realize the reasonable distribution of power. Finally, the effectiveness of the proposed control strategy was verified by simulation.