As electromagnetic environment of semiconductor device and integrated circuit deteriorates increasingly, electromagnetic pulse (EMP) of device and damage phenomenon have received more and more attention. In this paper, the damage effect and mechanism of the GaN high electron mobility field effect transistor(HEMT) under EMP are investigated. A two-dimensional electro-thermal theoretical model of GaN HEMT under EMP is proposed, which includes GaN polarization effect, mobility degradation in large electric field, avalanche generation effect, and self-heating effect. The internal transient response of AlGaN/ GaN HEMT is analyzed under the EMP injected into the gate electrode, and the damage mechanism is studied. The results show that the temperature of device keeps increasing, and the rate is divided into three stages, which present a tendency of rapid-slow-sharp till burn-out. The first rapid increasing of temperature is caused by the avalanche breakdown, and then rate becomes smaller due to the decrease of electric field. As the temperature is more than 2000 K, a positive feedback is formed between the hot electron emission and temperature of device, which causes temperature to sharply increase till burn-out. The maximum values of electric field and current density are located at the cylinder surface beneath the gate around the source, which is damage prone because of heat accumulation. Finally, the dependences of the EMP damage power, P, and the absorbed energy, E, on pulse width are obtained in a nanosecond range by adopting the data analysis software. It is demonstrated that the damage power threshold decreases but the energy threshold increases slightly with the increasing of pulse-width. The proposed formulas P = 38-0.052 and E = 1.1 0.062 can estimate the HPM pulse-width dependent damage power threshold and energy threshold of AlGaN/GaN HEMT, which can provide a good prediction of device damage and a guiding significance for electromagnetic pulse resistance destruction.