Because the particular photo-electricity of gold nanorods (Au NRs) presents a different characteristic than other types of Au nano-materials with various shapes, it has attracted much attention recently. Accurate measurement for aspect ratios does provide very high value on the optical property of Au NRs. Monte Carlo (MC) simulation is thought as the most accurate tool to perform size measurement through extracting structure parameters from the simulated scanning electron microscopy (SEM) image which best matches the experimental one. However, it has already been observed that the contrast of two ends of Au NRs in the experimental SEM image is brighter than that of middle part, which cannot be obtained by the conventional MC simulation approach. This phenomenon seriously affects the accuracy of size measurement for Au NRs. Therefore, in this article, a MC study was exerted on the frequently observed abnormal contrast of Au NRs. It was found that the cetyltrimethylammonium bromide (CTAB) which covers around the Au NRs indeed can alter the contrast of Au NRs comparing on that without CTAB covering. However, secondary electrons (SEs) emitting from CTAB is not the contributor for the abnormal brightness at two ends of NRs. The analysis reveals that the CTAB which covers around the Au NRs isolates Au NRs from the substrate, leading to charges accumulated in the body of Au NRs. The surface potential of Au NRs which produced by deposited charges presents a positive value and the potential value of the middle region is higher than that of both ends. Therefore, the SEs emitted from the middle region will be more easily attracted back to the surface than that emitted from both ends. As a consequence, the image contrast in the middle region of Au NRs is lower than that at both ends.