High-speed permanent magnetic generator (HSPMG) is a common and important power generation equipment in distributed generation systems. In this paper, a 100kW level HSPMG is studied, and the transient 2-D electromagnetic field is analyzed by using FEA, from which losses distributions (heat sources), especially eddy loss in rotor sleeve in machines are determined. Then, the 3-D thermal field is calculated, in which the variations of flowing state and temperature of fluid in stator ducts along the axial direction are considered, as well as its effects on motor temperature distribution. Based on this, the cooling system is optimal designed, and a new cooling ducts with variational cross section is proposed. The obtained conclusions may provide useful reference for the design and research of HSPMG.