Abstract: In response to the thermal management challenges of a highly integrated electronic equipment module of a certain type of seeker under extreme working conditions, an optimal design method for the structural heat sink based on barium hydroxide octahydrate phase change material is proposed in this paper. Through the finite element analysis method, the influence laws of four gradient thermal conductivity enhancement configurations on the heat storage performance are studied, with a focus on revealing the coupling mechanism between the distribution density of the heat conduction ribs and the heat flow transmission characteristics. Based on the collaborative optimization of heat transfer enhancement and heat storage capacity, the composite structure of 16-grid heat conduction fin combined with a central cylindrical fin is determined as the best solution. The equivalent thermal conductivity of the phase change material is increased by 2.66 times. An experimental platform is built for verification, and the results show that the effective temperature control time of the optimized phase change heat sink differs from the simulation results by only 3.2%, and the phase change equilibrium temperature deviates by only 2 °C. This study provides a design concept that combines high energy storage density and efficient heat diffusion for the transient thermal management of missile-borne electronic equipment.