The internal pore structure 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 it difficult to visually present in the mesoscopic numerical model of concrete. Therefore, based on the physical mechanism of ice crystal phase transition in pore water and the specific surface friction mechanism of porous seepage, this paper establishes an estimation model for effective thermal conductivity and permeability coefficients that can reflect the distribution characteristics of internal pore size and the content of microbubbles in porous media, and explores the evolution mechanism of effective thermal conductivity and permeability coefficients with the freezing process. In addition, a switching model for 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 assigned to the cement mortar and interface transition zone (ITZ), and a thermal-hydraulic-mechanical coupling finite element model of concrete specimens at 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 relief mechanism of microbubbles on pore pressure and the deterioration 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.