Pneumatic down-the-hole (DTH) hammer drilling technology has been used extensively in the fields of heat reservoir exploitation and geological exploration owing to its advantages of high efficiency and low pollution. However, the vibration near the bit is up to 40 g while DTH hammer drilling, which significantly affects the performance and longevity of the near-bit measurement while drilling (MWD). To enhance the environmental adaptability of the near-bit MWD in pneumatic DTH operations, a design method for a vibration-damping system based on the parameter optimization of a non-dominated sorting genetic algorithm II (NSGA-II) is proposed in this study. First, the whole structure of the near-bit MWD is designed, including the MWD sub-shell, sensors, measurement circuits, batteries, and connecting structures (the circuit unit). Secondly, this study analyzes the vibration characteristics of the pneumatic DTH hammer near the bit. According to the damping structure, the vibration response model for the circuit unit and the damping model are established. Thirdly, NSGA-II is employed to optimize the parameters of the damping model in terms of the low-frequency, high-intensity vibration characteristics near the bit in pneumatic DTH operations, thereby devising a damping scheme tailored to the unique conditions of DTH hammer drilling. Finally, vibration experiments were conducted to verify the effectiveness of the vibration-damping device. The experimental results indicate that within the vibration frequency range of 5–20 Hz and vibration level of 10–40 g, the peak attenuation rate of the circuit unit is more than 86.446%, and the improvement rate of the vibration stability of the system is more than 75.214%; the anti-vibration performance of the near-bit MWD system in DTH hammer drilling is improved remarkably. This study provides strong technical support for the stability of MWD equipment under such special working conditions. It has broad engineering application prospects.