The vulnerability of microcontroller system against high-altitude electromagnetic pulse (HEMP) is taken as an illustration to demonstrate the assessment methodology based on Bayesian networks (BN). The complete procedure is performed by two steps: the qualitative and the quantitative. The first step focuses on the analysis of three classes of properties, the electromagnetic environment, system function/structure, and their interactions. The primary BN model is built at the end of the first step. The second step investigates the BN nodes and branches one by one, which further implemented through two stages, i.e., the data acquisition and data fusion. The susceptibilities of devises are examined with the pulsed current injection. The responses of the transmission lines to HEMP are computed using the field-line coupling model. Comparing the probability density functions of the electromagnetic stresses and strengths produces the failure probabilities of the interface components. Through two-step analysis, the critical elements and coupling paths are identified and highlighted. After neglecting those unimportant factors, many BN nodes and branches are deleted. Thus, the complexity of assessment is reduced. By assigning the probability values to the simplified BN model, the system failure probability is calculated, which characterizes the system vulnerability against HEMP environment. The illustration validates the rationality and flexibility of the BN assessment methodology.