The effects of porosity and pore distribution on the heat transfer performance of polyimide (PI) aerogel under natural convection were investigated through a combination of experimental and numerical simulations. The governing equations of heat transfer were analyzed in detail. A novel heterogeneity factor (η) was introduced to quantify internal pore distribution. PI aerogels exhibiting a range of porosities and heterogeneity factors were synthesized and characterized. The natural convection heat transfer coefficient of PI aerogels was measured experimentally, providing empirical data. A porous model was developed by integrating Voronoi technique with a two-scale generation method, allowing for comprehensive numerical simulations of heat transfer. The numerical results demonstrated strong concordance with the experimental data, validating the model’s accuracy. The results revealed that the heat transfer performance of the aerogels diminished markedly with increasing porosity when heterogeneity was held constant. Conversely, with fixed porosity, the heat transfer performance improved significantly with greater heterogeneity. Numerical simulations further enabled the visualization of internal temperature and flow fields, elucidating that the effect of porosity and heterogeneity on natural convection heat transfer performance is predominantly driven by variations in internal permeability.