Nanoprobing is an indispensable method for failure analysis to identify failure cells and to approach the root causes, providing electric characteristics of the failure of the MOS transistor. In this paper, the characteristic degradation on MOS transistors with SEM-based nanoprobing is studied to find out the critical accelerating voltage, comparing it to the characteristic obtained by the mechanical prober. In this experiment, n-type MOS transistors with thick gate oxide layer (40nm) were used. The effect of electron beam irradiation was also investigated. Significant change was not observed in n+(drain)/p-well IV curves. The paper looks at the influence of the additional phenomena during SEM-based nanoprobing analysis on a characteristics change of a specimen. For MOS transistor with thick gate oxide used in this study, irradiation influence is possibly more notable than normal voltage cell cases.