The effect of water distribution on heat conduction in unsaturated structural clayey soils with double porosity system is investigated in the present study. A dual-porosity model consisting of intra-aggregate and inter-aggregate pores is developed to describe the water distribution within intra-aggregate and inter-aggregate pores. Heat transfer using this model is then numerically simulated to determine the soil effective thermal conductivity. The obtained values are compared with available experimental data. The results show that the model can predict the accurate soil thermal conductivity values at various water contents and densities. On one hand, the model shows a higher soil thermal conductivity when water content and/or dry density are higher. On the other hand, the model shows an effect of water distribution on the soil thermal conductivity; this later is higher when water is preferentially distributed within aggregates than between aggregates. In addition, the model can give a direct visualization of heat transfer mechanisms in unsaturated clayey soils with double porosity system. In fact, heat conduction is dominant in the wet region of the dual-porosity space. This study provides both a useful predictive model of thermal conductivity and a better understanding on the physical mechanism of heat conduction in unsaturated structural clayey soils or other multiphase media with double porosity system.