To enhance the reliability of the logging-while-drilling (LWD) neutron generator in harsh environments, this paper proposes a novel polymer monolithic potting protection scheme that can effectively decrease response of the structure under vibrational excitation by selecting suitable polymer potting material and installation method. This paper systematically evaluates the influence of viscoelastic parameters of the polymer potting material on vibration energy dissipation through theoretical calculations. Additionally, it thoroughly investigates the influence of the coupling between the potting modulus and the installation method on the reliability of the structure through finite element analysis. The results demonstrate that potting material with a shorter high-frequency relaxation time can more effectively absorb vibration energy. As the potting modulus increases, the maximum stress of the neutron tube decreases by 96.4%, 93.7%, and 84.7% under short-span, medium-span, and long-span installation methods, respectively. The maximum strain also decreases by 96.6%, 93.9%, and 86.5% respectively. By using the short-span support and high modulus potting material, the local stress and strain can be minimized. A prototype vibration test verifies the effectiveness of this method in improving the reliability of the neutron generator. This analysis provides a reference and reliability prediction for the design of future LWD neutron generators.