The transport property is a key factor with regard to the durability and service life of construction materials. It is of importance to establish a computer model to predict the transport properties of cement based materials on the basis of its microstructure coupled with a certain algorithm. First, the virtual microstructure of cement paste was obtained by a numerical model, which was converted to a discrete one represented by voxels. Then a three dimensional(3D) transport network was obtained according to the voxel represented microstructure. The flux through cement paste, the concentration distribution and the diffusion coefficient of cement paste under a given ion concentration boundary condition was calculated. Finite difference method(FDM) and conjugate gradient method(CGM) was compared in solving matrix equations and it was found that CGM is more efficient. Finally, the proposed model is validated by use of experimental data from steady state chloride diffusion test, and is applied to predict the chloride diffusion coefficients of cement paste with different water to cement ratio and at various hydration days.