This study proposes a multiscale prediction method that couples the DTW-CEMHYD3D hydration kinetics model with Mori–Tanaka homogenization theory to establish a quantitative relationship between hydration microstructure evolution and macroscopic heat and mass transport properties of cement-based materials. First, dynamic time warping (DTW) is introduced to correct the mapping relationship between the hydration cycle number in CEMHYD3D and the real hydration time. Then, cement-based materials are regarded as multiphase composites, and a unified calculation method for the effective diffusion coefficient and thermal conductivity is established. The results show that the DTW-CEMHYD3D model can markedly improve the prediction accuracy of early-age hydration heat. The average relative error between the predicted effective diffusion coefficient and the N-phase sphere model is 0.67%, while the coefficients of determination for thermal conductivity prediction and relative diffusion coefficient prediction during hydration reach 0.9812 and 0.987, respectively. Parametric analysis indicates that a higher water-to-binder ratio significantly increases the relative diffusion coefficient, and this effect exhibits nonlinear enhancement with hydration age. The influence of fly ash content is age-dependent. An increase in the degree of saturation reduces the chloride diffusion coefficient but only slightly increases the thermal conductivity. The proposed method provides a reference for durability analysis and parameter determination in multiphysics coupling models of cement-based materials.