The invention discloses a distributed hierarchical control method for a flywheel matrix system applied to a wind power plant, and a control method for a flywheel energy storage system applied to wind power plant, and particularly relates to a cooperative control method for the hierarchical structure of a flywheel energy storage matrix system applied to wind power plant. The distributed hierarchical control method comprises the following steps of: establishing the communication topological structure of each flywheel energy storage unit at first, and then constructing a multi-agent-based distributed upper-layer power allocation algorithm, determining the own charge-discharge state and power of each flywheel by allocating the total reference power of the system in a ratio according to the exchange information of each flywheel and the neighbours thereof, and submitting the calculated results to a local controller to execute, so as to realize the purpose of the invention; therefore, the distributed hierarchical control method has real-time performance, and can reduce construction cost, improve system flexibility, reduce system computation complexity, and enhance system robustness and fault tolerance.