Being a promising method for thermal protection system, transpiration cooling has received wide interest recently. Numerical simulation for transpiration cooling, however, has been limited due to the mis-matching between the pore-scale two-phase flow and external high-temperature aerothermodynamic environment, which induced by conventional decoupled or iterative one-way coupled simplification methods. In this work, a fully coupled continuum-scale and pore-scale model is established for transient transpiration cooling at the interface between boundary layer flow and porous medium through coupling Computational Fluid Dynamics (CFD) and Pore-Network Model (PNM), termed as the multiscale CFD-PNM coupled method. The coupled method allows to capture detailed displacement and phase change of two-phase flow at pore-scale, revealing the strong interaction of the water vapor with the external free flow within a high temperature boundary layer. After successfully validating the new coupled model by comparing with the Two-Phase Mixture Model (TPMM) solution, a number of cases mimicking the cooling at the interface of typical blunt bodies are simulated. The results show that the multiscale CFD-PNM coupled method can not only provide the thermal protection effect prediction, but also reveal many critical features that beyond the reach of continuum-scale studies. Some pore-scale phenomena that are important to the overall transpiration cooling effects are revealed, including transient phase change and composition variation of water vapor, imbibition and drainage of two-phase flow related to pore-scale capillary thresholds and applied boundary pressures, as well as the two-way mass transfer at the interface, such as the invasion of external hot air.