This paper proposes the performance analysis model of switched flight control systems driven by the digital upsets when electronics devices are subject to electromagnetic environments. Hidden Markov Model (HMM) is used to describe the characteristics of digital upsets and construct the model based on the theory of the electromagnetic interferences. The parameter estimation algorithms of the traditional training method for HMM are sensitive to initial parameters, therefore, this paper proposes a fast initial parameter selection strategy which can also accelerate the training processes. At the end, HMM-based electromagnetic interferences are fed to the performance observation platform for the distributed flight control systems. This paper also compares multiple performance degradation results under different electromagnetic fields from theory and simulation perspectives. Simulation results demonstrate HMM model can characterize the digital electromagnetic upsets more accurately compared to the existed digital electromagnetic models, and simulation results of the corresponding performance degradation are consistent with the theoretic results.