High-power microwave (HPM) affects the normal operation of electronic devices or systems, and the effects are related to the parameters of the microwave pulse. To the best of our knowledge, there are no reported studies on the effect of HPM pulse width and repetition frequency on the autonomous aerial vehicles (AAV) system. The mechanism of the effect of pulse width and repetition frequency on the electromagnetic coupling of electronic systems is unclear. For this reason, this article takes the typical AAV system as the example and investigates the effect of C-band HPM pulse width and repetition frequency on it. HPM irradiation tests on the AAV are carried out and it is found that the GPS receiver, datalink and flight control module are susceptible to be affected and fail to operate normally. In addition, the test results show that the probability of the sensitive device being affected increases with the increase of pulse width and repetition frequency. Moreover, a simulation study of the flight control module subjected to HPM irradiation is conducted and it is found that voltage pulses can be coupled to the cable connected to the flight control circuits, which may affect the normal operation of the circuits. In order to further investigate the mechanism of the effect of pulse width and repetition frequency, an equivalent circuit model is established. It is observed that the voltage across sensitive device loads increases with wider interference signal pulse and higher repetition frequency. This leads to the devices being more susceptible, which is consistent with the test results.