With the continuous development of society, more and more people pay attention to energy issues, and the realization of energy storage has become a hot research direction today. Despite advancements, the control system of the high-speed flywheel energy storage system’s permanent magnet motor still encounters issues in effectively regulating the magnetic suspension bearing and motor speed. In addressing this issue, a technical solution involves the implementation of an intelligent control system for the high-speed flywheel energy storage system’s permanent magnet motor, utilizing deep learning principles. This innovative approach employs deep neural networks to model, optimize, and regulate the flywheel energy storage system. The essence of flywheel energy storage lies in the conversion of electrical energy into mechanical energy, followed by its reconversion into electrical energy during output. It has the advantages of high energy density, high power density, long cycle life, fast charging and discharging, maintenance-free and environmental protection. A permanent magnet motor is a motor that uses permanent magnets to generate a magnetic field. It has the characteristics of high efficiency, high power density, and low rotor loss. It remains the most widely utilized motor in flywheel energy storage systems. An intelligent control system is characterized by its use of artificial intelligence technology to adapt, self-learn, and self-organize complex systems. This system is distinguished by its robust nonlinear processing capabilities and resilience to faults. The high-speed flywheel energy storage system permanent magnet motor intelligent control system based on deep learning can improve the performance, efficiency and reliability of the flywheel energy storage system, reduce costs and risks, and is suitable for electric vehicles, rail transit, power grid frequency regulation and other fields. In this paper, the convolutional neural network and PSO algorithm are used to obtain the PSNN neural network structure to predict the speed of the motor, so as to achieve its control. And the reliability of the structure is verified by experiments.