Water permeability is a key property for the serviceability and durability of concrete structures, which governs the transport of fluid through the pore network in the cementitious material. A microstructure-based numerical test method is proposed and employed to predict the permeability of hydrating cement paste. Numerical samples characterizing the evolution of the microstructure of cement paste are generated using the computational code HYMOSTRUC3D. Based on the three-dimensional (3D) finite element method (FEM), the pore-scale flow of water induced by pressure-gradient through the sample is simulated and the corresponding permeability is estimated. Water flow characteristics in the hydrating cement paste and the evolution of the permeability against different water-to-cement ratio (w/c), porosity, curing age and degree of hydration are investigated by numerical simulations. The simulated results are verified in comparison with available theoretical solutions, experimental data and numerical predictions obtained from the literature. Due to the dilution and tortuosity effects, the permeability decreases with the increase of cement hydration and the decrease of w/c. The connectivity of the pore throat plays an important role in affecting water movement in hydrating cement paste. The developed modeling approach is capable to investigate the transport properties of cement paste, which may provide basic parameters for multiscale modeling of concrete performance and strongly support the coupled multiphysics analysis in concrete engineering.