Predicting transport properties of cement-based materials directly from the microstructure is very challenging, due to the problems of bridging length scales and the difficulties of realistically representing the microstructure. Based on a two-scale representation of the microstructure, a scheme is proposed in this paper to model the transport properties of cement paste through two-scale random walk simulation. A random walk algorithm is firstly applied at the sub-micro-scale to determine the diffusion tortuosity of the outer C-S-H layer. This is then up-scaled to the micro-scale to compute the diffusion tortuosity of cement paste. Based on physical laws, the diffusion tortuosity is transformed into the formation factor, and further into the electrical conductivity and the chloride diffusion coefficient of cement paste, and subsequently validated. It is proven that a more realistic representation of the microstructure makes it possible to derive transport properties of cement paste, directly and accurately, from the microstructure.