With the development of microelectronic technology, the integration of electronic systems is increasing continuously. Electronic systems are becoming more and more sensitive to external electromagnetic environments. Therefore, to improve the robustness of radio frequency (RF) microwave circuits, it is crucial to study the reliability of semiconductor devices. In this paper, the temporary failure mechanism of a gallium arsenide (GaAs) pseudomorphic high electron mobility transistor (pHEMT) in a navigation low-noise amplifier (LNA) under the jamming of ultra-wideband (UWB) electromagnetic pulses (EMP) is investigated. The failure process and failure mechanism of pHEMT under UWB EMP are elaborated by analyzing the internal electric field, current density, and temperature distribution. In detail, as the amplitude of UWB EMP increases, the output current, carrier mobility, and transconductance of pHEMT decrease, eventually resulting in gain compression. The injection experiment on LNA, which effectively verified the failure mechanism, indicates that the gain of pHEMT is suppressed instantaneously under the jamming of UWB EMP and the navigation signal cannot be effectively amplified. When UWB EMP amplitude increases to nearly 10 V, the BeiDou Navigation Satellite System (BDS) carrier signal is suppressed by nearly 600 ns. Experimental results accord well with the simulation of our model. UWB EMP jamming is a new and efficient type of electromagnetic attack system based on the device saturation effect. The performance degradation and failure mechanism analysis contribute to RF reinforcement design.