Due to the presence of tiny gaps at the interface of two layers of saturated soil, water seepage occurs at a slower rate within these gaps, resulting in laminar flow at the interface. Based on the Hagen‐Poiseuille law, a general imperfect flow contact model was established for layered saturated soil interfaces by introducing the flow contact transfer coefficient Rω and the flow partition coefficient ηω. The investigation focused on the thermal consolidation behavior of layered saturated soil foundations under variable loadings considering the flow contact resistance effect at the interface. By employing the Laplace transform and its inverse transform, a semi‐analytical solution for the thermal consolidation of layered saturated soil foundations was derived. In the context of a two‐layer soil system, the effects of Rω, ηω, and permeability coefficient k on the consolidation process were examined. The obtained results were then compared with three other interfacial contact models, thereby confirming the rationality of the presented model. The study findings revealed that the flow contact resistance effect leads to a clear jump in the pore water pressure. Furthermore, an increase in Rω and a decrease in ηω were found to significantly enhance displacement and pore water pressure, while having minimal impact on the temperature increment. These insights contribute to a more comprehensive understanding of the thermal consolidation behavior of layered saturated soil foundations and underscore the significance of accounting for the flow contact resistance effect in such analyses.