Abstract: During the operation of a neutron generator, D⁺ ions are accelerated and bombarded onto the titanium target. During the high-energy beam bombardment, secondary electrons are emitted from the target surface, increasing the power supply load and affecting the stability of the system. This study investigates the effects of different electrode structures on chamber temperature, vacuum level, and neutron yield. The results show that the shape of the electrode waist hole directly influences the number of secondary electrons escaping through the hole, which further affects the chamber wall temperature. This leads to the release of adsorbed gases from the wall, increasing the frequency of high-voltage arcing. The transmission paths of secondary electrons were analyzed. Simulations indicate that some sputtered secondary electrons from the target surface escape through the waist hole and strike the chamber wall, some impact the inner side of the electrode, and a small portion are accelerated in reverse to hit the ceramic window. These simulation results are consistent with observed physical traces. Based on these findings, experiments were conducted to suppress secondary electrons using resistors and magnetic fields. Results show that a 30−68 kΩ resistor effectively suppresses secondary electrons, achieving a higher neutron yield at a relatively lower current. Additionally, a 1.3 T remanent permanent magnet was used to create a magnetic field of about 100 Gs at the center, which effectively deflects secondary electrons, reducing current by approximately 23% without impacting neutron yield. This demonstrates effective secondary electron suppression. Overall, maintaining the internal vacuum within the electrode, minimizing or avoiding openings on the electrode wall, and implementing effective secondary electron suppression measures can improve the stability of the neutron generator, thereby extending its service life.