In this work, we conducted a mechanistic study on pore‐scale mechanisms controlling heat transfer in partially saturated porous media at unfrozen and frozen conditions. Experimental measurement of effective thermal conductivity (ETC) of simulated partially saturated sediments was carried out to explore the effect of different parameters including pore and overburden pressures, temperature, and water/ice saturation on the pore‐scale mechanisms governing heat transfer in multiphase porous media. The experimental measurements show that the heat transfer is a complex phenomenon affected by several important pore‐scale mechanisms such as particle‐particle conduction and particle‐fluid‐particle conduction, which are governed by water content and distribution, packing structure, wettability characteristics of grains, coordination number, and physical contact among sediment particle. A numerical model was also developed for prediction of ETC using free‐energy lattice Boltzmann model and a space renormalization method. The model predictions were in good agreement with the experimental data, showing that the model is able to reliably estimate ETC with average relative deviations of less than 10%, as it appropriately incorporates the pore‐scale mechanisms influencing ETC. The numerical model predictions were also compared with those of six predictive models available in the literature, and root‐mean‐square errors were calculated to assess its accuracy against the existing models.