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High-speed permanent-magnet generators (HSPMGs) are common and important power generation equipment used in distributed generation systems. A 100-kW-level HSPMG is investigated in this paper, and its cooling system is optimized through electromagnetic-fluid-thermal analysis. First, the 2-D electromagnetic field of the machine is calculated by using the time-stepping finite element method, and the electromagnetic performance and loss distributions (heat sources) are determined, particularly the eddy loss of the rotor sleeve. Then, a thermal analysis model of the fluid for the HSPMG is established. Through numerical calculating, the whole region 3-D temperature distribution in the HSPMG is obtained, in which the influence of temperature on material properties is considered. Considering the variations of heat transfer abilities of the cooling medium, the temperatures in machines with different cooling structures are comparatively analyzed, and new cooling grooves with variable cross sections are proposed, which make the temperatures in the machine lower and more evenly distributed. The obtained conclusions may provide useful reference for the optimal design and research of HSPMGs.