The paper demonstrates that the electron beam (e-beam) irradiation induced charging-effect has remarkable impact on nanoprobing localization of a crystal defect hidden in metal-oxide-semiconductor field-effect transistor (MOSFET). We present a practical example showing that device characterization at the contact layer (CT) is susceptible to the charging-effect since scanning electron microscopy (SEM) based nanoprobe system running is inevitablely acompanied by e-beam irradiation towards device under test (DUT). The mechanisms is seldomly reported in the past. In our case, the p-n junction at a nMOSFET drain end showed the ohmic current-voltage (I-V) characteristic at the beginning. However, by utilizing the atomic force microscopy (AFM) based nanoprobe system without e-beam, the measurement found previous resistive characteristic of the p-n junctions disappeared. Instead, it exhibited good rectifying characteristic. I-V characteristic discrepancy coming from two analytical methods was attributed to the charging-effect influence. It was experimentally proven that the charging-effect impact at MOSFET gate CT had strong dependance on the e-beam irradiation magnitude corresponding to the SEM scan speed. Charging effect produced distinct consequences at distinct scan speeds. The positive charging-effect occurred under the fast scan while the negative charging-effect occurred under the slow scan. The former mechanism made the potential at gate CT high enough to turn on nMOSFET. Therefore, the nMOSFET channel current merged with the p-n junction current in a closed-loop. In contrast, the slow scan induced negative charging-effect made the gate potential lower than the nMOSFET threshold voltage (VT), so that the nMOSFET stayed off-state. Consequently, the p-n junction resumed its intrinsic rectifying I-V characteristic. Different from the nMOSFET, the charging-effect affected the pMOSFET in the opposite manner. As a result, the initial conclusion of the MOSFET junction leakage was not valid. Next, we ran a optimal flow to narrow down a fault by eliminating the charging-effect impact. Eventually, a crystal defect (pipeline) was isolated in a suspcted nMOSFET relying on nanoprobe and TEM analysis. The article explains the evident influence of charging-effect on the nanoprobe analysis and puts forward an effective way to minimize the side effect of the e-beam irradiation. The work may draw more attention to the analytical methodologies regarding MOSFET reliability improvement.