Embodiments provide systems and methods for analyzing effects of cargo fire on primary aircraft structure. A thermal profile of a suppressed fire in a cargo compartment of an aircraft is developed. The thermal profile is applied to a heat transfer model of structure of an aircraft, and structural integrity of the modeled structure is analyzed. The thermal profile may be developed by introducing a fire in a physical model of a cargo compartment instrumented with temperature sensors and determining profiles of temperature versus time. A heat transfer model of aircraft structure is built, boundary conditions are input into the heat transfer model, and the model is run. When analysis of the modeled structure determined structural integrity to be insufficient to satisfy flight certification requirements, structural parameters are modified, the thermal profile is applied to a heat transfer model of the modified structure, and the analysis is repeated.