On-board flywheel energy storage device has attracted widespread attention due to its high efficiency and pollution-free advantages. The motor is the core component of the energy conversion of the flywheel energy storage device, and the size of its loss directly restricts the motor speed, which in turn affects the performance of the flywheel energy storage system. This paper gives the specific calculation formulas of iron loss and permanent magnet eddy current loss of permanent magnet-assisted synchronous reluctance motor, and analyses the influence factors of the two types of losses. Based on the ascertainment of the influence laws of the motor structure parameters on the performance of the torque electromagnetic system and the performance of the loss system, the non-sensitive variables, single-system sensitive variables and double-system sensitive variables are classified and defined. The Taguchi method is further used to optimize the design of the rotor structure with sensitive parameters by performing torque and electromagnetic analysis on several key parameters of the motor rotor. Based on the optimal torque design, progressive torque-loss dual-system co-optimization is performed to obtain the optimal motor parameter configurations under the constraints of electric-magnetic-loss coupling in the final calculation.