In addressing the shortcomings of conventional thermal management systems for aircraft instrument compartments, including high mass, large volume occupation, poor reusability, and high costs, this paper focuses on the instrument bay structure. It proposes a design scheme for an instrument compartment structure based on phase change materials, leveraging the heat transfer characteristics of these materials. On this foundation, a one-dimensional phase change heat transfer theoretical model is constructed, and the phase change heat transfer equation is solved using the Green's function method. Through comprehensive research and analysis of the one-dimensional phase change heat transfer mechanism, the thermal laws of phase change heat transfer are revealed. To validate the accuracy of the theoretical models and explore the temperature variation patterns within the instrument cabin structure, this paper carries out a thermal experiment on the instrument compartment structure. The experimental results demonstrate that, compared to an instrument compartment structure composed entirely of aluminum alloy, an instrument compartment structure filled with phase change materials can more effectively reduce the temperature of the structure itself. Additionally, the numerical calculations obtained from the devised one-dimensional phase change heat transfer model demonstrate a commendable agreement with the experimental data, thereby affirming the accuracy of the theoretical model.