The temperature of electronic equipment in the payload compartment of an airship greatly affects its operational reliability. As the application scope of the airship payload compartment expands, the total power of the payload continues to increase, leading to significant increases in equipment design power consumption and heat flux density. However, the density of the atmosphere in the stratosphere is only 1/18 of that at the ground level, resulting in poor convective heat dissipation capability. Heat dissipation has gradually become a key issue restricting technological development. To address the thermal pain points under high payload power, this article introduces the two-phase fluid loop heat dissipation method and explores its heat dissipation capability compared to fan-forced heat dissipation. Based on the analysis of the heat transfer characteristics of electronic equipment in the payload compartment, a fan-forced convection heat dissipation system is designed based on computational fluid dynamics. Simultaneously, a method for using a 1,1,1,2-tetrafluoroethane (R134a) fluid loop to dissipate heat in the stratospheric payload compartment for electronic equipment is proposed, and its simulation is conducted using the apparent heat capacity method. The temperature and flow fields of the airship payload compartment under the two heat dissipation methods are calculated, obtaining the heat dissipation capabilities of the two methods. Simulation results indicate that the heat dissipation limit of the fan is approximately 591 W, while the two-phase fluid loop heat dissipation method can meet the heat dissipation requirement of 700 W, thus fulfilling the basic heat dissipation needs. The use of the two-phase fluid loop heat dissipation method can effectively control the temperature of electronic equipment in stratospheric airship payload compartments, providing insights into the design and calculation of heat dissipation for high-power electronic equipment in the stratosphere.