In a small centrifugal compressor system, a high-speed motor needs to be developed to drive impellers directly. Heat is generated by both electrical heating due to copper coil resistance and aerodynamic heating in the gap between the rotor and stator in a high-speed motor. Removal of the heat is essential to the design of such motors since most magnetic materials are brittle and can be easily fractured by the heat. In the present study the cooling flow fields and temperature distributions are analyzed by using computational fluid dynamics simulation for a high-speed motor which has air cooling system as well as water cooling system. In the analysis, a conjugate heat transfer problem is solved by considering both convective heat transfer in the cooling system and conduction heat transfer in solid parts. Based on design drawings of a motor, air cooling system and water cooling system are analyzed to obtain temperature field and thus to check the coiling system performance. Also the cooling performance are studied for various flow rates of cooling air and water at the inlets.