In this study, the effect of variable cross-section wicking core structures on the performance of heat transfer systems was investigated. A capillary core model of a porous medium was established by using the COMSOL simulation software. After theoretical verification, it was studied how the overall geometric shape affects the comprehensive performance of the integrated capillary core and its resistance to acceleration loads. By comparing the liquid filling times of different structured suction cores, it is known that the overall capillary performance of the variable cross-section core is superior to that of the traditional constant cross-section core. Specifically, the suction core at the evaporation end, which has the same structure as the original suction core, has a better heat transfer efficiency, but its start-up time will be prolonged. Furthermore, variable cross-section wicking cores with identical total volume as their uniform counterparts enhance resistance to acceleration loads and decrease filling time while maintaining effective heat transfer. These findings provide a theoretical foundation for the structural optimization of wicking cores in heat transfer systems.