Brushless direct current (BLDC) permanent magnet (PM) synchronous motors are in high demand for ventilator applications owing to their high speed, high efficiency, and other significant features. However, it has become an important problem in eddy current loss calculations with high-speed motors, which leads to low motor (ventilator) life and PM demagnetization. This paper focuses on the eddy current loss calculation and the structure improvement design for the two-pole 90 W, 47,000 r/min toothless BLDC motor. First, the influencing factors of eddy current loss are comprehensively investigated, and a multiparameter improvement methodology is proposed accordingly. Second, by finite element analysis (FEA), the effective winding length ratio and the number of parallel wires were mainly researched for the winding, and the influence on the eddy current loss and the efficiency was determined, providing a reference for BLDC high-speed motors. This study has resulted in a 34.75% reduction in the winding losses, and a 4.6% increase in the efficiency of the improved model compared with the original design. Third, the new rotor structure is proposed, saving PM volume 15% more than original. THD of gap flux density is decreased 20.97%; the eddy current loss in the new rotor is decreased 22% more than original. Furthermore, by coupling simulation of the magnetic–thermal field, the maximum temperature of winding of the improved model is 13.4% lower than that of the original model at the thermal steady state. Finally, the electromagnetic and thermal properties simulation results were verified by testing the prototype. It is of great significance to the structure design and efficiency improvement of the BLDC high-speed motor.