The response of a bipolar transistor (BJT) under a square-wave electromagnetic pulse (EMP) with different injecting voltages is investigated. Adopting the curve fitting method, the relationship between the burnout time, the damage energy and the injecting voltage is obtained. Research shows that the damage energy is not a constant value, but changes with the injecting voltage level. By use of the device simulator Medici, the internal behavior of the burned device is analyzed. Simulation results indicate that the variation of the damage energy with injecting voltage is caused by the distribution change of hot spot position under different injection levels. Therefore, the traditional way to evaluate the trade-off between the burnout time and the injecting voltage is not comprehensive due to the variation of the damage energy.