The internal pore structural characteristics and microbubble distribution features of concrete have a significant impact on its frost resistance, but their size is relatively small compared to aggregates, making them difficult to visually represent in the mesoscopic numerical model of concrete. Therefore, based on the ice-crystal phase transition mechanism of pore water and the theory of fine-scale inclusions, this paper establishes an estimation model for effective thermal conductivity and permeability coefficients that can reflect the distribution characteristics of the internal pore size and the content of microbubbles in porous media and explores the evolution mechanism of effective thermal conductivity and permeability coefficients during the freezing process. The segmented Gaussian integration method is adopted for the calculation of integrals involving pore size distribution curves. In addition, based on the concept that the fracture phase represents continuous damage, a switching model for the permeability coefficient is proposed to address the fundamental impact of frost cracking on permeability. Finally, the proposed estimation models for thermal conductivity and permeability are applied to the cement mortar and the interface transition zone (ITZ), and a thermal-hydraulic-mechanical coupling finite element model of concrete specimens at the mesoscale based on the fracture phase-field method is established. After that, the frost-cracking mechanism in ordinary concrete samples during the freezing process is explored, as well as the mechanism of microbubbles in relieving pore pressure and the adverse effect of accelerated cooling on frost cracking. The results show that the cracks first occurred near the aggregate on the concrete sample surface and then extended inward along the interface transition zone, which is consistent with the frost-cracking scenario of concrete structures in cold regions.