Abstract: Determining the full-energy peak efficiency (FEPE) of a high-purity germanium (HPGe) detector through experimental methods or Monte Carlo (MC) simulations is crucial for accurate radionuclide quantification. This study presents a meticulously constructed MC model tailored to the actual dimensions of the measured HPGe crystal. Optimization of the dead layer thickness within the model was achieved through an integrated approach of experimental validation and simulation efforts, yielding a minimal average relative deviation of 1.74% between simulated and actual detection efficiencies. Subsequent simulations were conducted to assess the impact of structural modifications in the HPGe crystal and variations in the diameter of copper electrode rods on FEPE. The findings indicate that low-energy gamma rays exhibit increased sensitivity to modifications at the crystal’s top, with the rounded edges displaying a substantial relative deviation in detection efficiency of up to 19.21% at 59.5 keV. Additionally, the presence of a protective ring at the crystal’s base significantly enhances the detection efficiency for high-energy rays as incident energy and source distance increase, while its impact on low-energy rays remains minimal. Changes in the diameter of the copper electrode rods, which act as ray-blocking devices, were found to decrease the detection efficiency of high-energy rays by as much as 1.78%. These insights are pivotal for refining detector design and advancing the calibration precision of FEPE in scientific applications.