It is a research hotspot of electric propulsion system that a high energy density permanent magnet machine is used as its main power. In general, the power system of electric propulsion consists of batteries, inverters and high energy density permanent magnet machines and loads. Based on harmonic effect of PWM sine alternating current generated by inverter, iron loss model of high energy density permanent magnet machine is established under inverter power harmonic, and iron loss calculation flow chart of high energy density permanent magnet machine for electric propulsion system is shown. The influences of different stator outer diameter and rotor inner diameter on iron loss are analyzed by using the finite element method. Through the above analysis, a 30 kW high energy density permanent magnet machine was designed. Then the noload test and iron loss separation test were carried out, verifying that the machine has very low core loss.