Heat pipe–cooled microreactors are a promising innovation for nuclear power generation because of their reliable passive heat transfer capabilities. However, concerns related to creep failure and differential thermal expansion pose significant challenges, potentially leading to structural failure and radioactivity release. Additionally, startup challenges, such as ensuring consistent heat transfer during initial reactor operation and managing transient thermal conditions, also need to be addressed to achieve reliable performance. The helium gap can provide benefits during the startup process by enhancing thermal insulation, which helps in controlling the heatup rate and reducing thermal stresses; thereby, it helps to have more stable and consistent reactor startup. This protective gap also helps in minimizing the likelihood of radioactive release by maintaining the structural integrity of the reactor components. This study explores the impact of the helium gap, the space between the condenser wall and the sleeve tube, on the thermal performance of heat pipes and an axial flow heat exchanger. A numerical approach is employed to evaluate how variations in the helium gap affect thermal resistance, heat transfer efficiency, and overall system performance. Results show that the helium gap thickness significantly affects the heat pipe’s performance. A thickness of 0.0065 cm or 0.015 cm improves startup performance, while 0.1 cm has a negative impact. Adding a helium gap may slightly reduce system power output by lowering the coolant temperature in the heat exchanger. However, using an optimal helium gap thickness appears to be a promising design strategy to enhance both the safety and performance of heat pipe–cooled microreactors.