Permeability coefficient of concrete is a substaintial key parameter for understanding the durability performance of concrete and its microstructural densification. Many researches for the issue have been accomplished, however, it is very rare to deal with the theoretical study on permeability coefficient in connection with carbonation of concrete and the the effect of volumetric fraction of cement paste or aggregate on the permeability coefficient. The majority of these researches have not dealt with this issue combined with carbonation of concrete, although carbonation can significantly impact on the permeability coefficient of concrete. The purpose of this study is to establish a fundamental approach to compute the permeability coefficeint of (non)carbonated concrete. When simulating a microstructural characteristics as a starting point for deriving a model for the permeability coefficient by the numerical simulation program for cementitious materials, HYMOSTRUC, a more realistic formulation can be achieved. For several compositions of cement pastes, the permeability coefficient was calculated with the analytical formulation, followed by a microstructure-based model. Emphasis was on the microstructural changes and its effective change of the permeability coefficient of carbonated concrete. For carbonated concrete, reduced porosity was calculated and this was used for calculating the permeability coefficeint. The computational result was compared with experimental outcome.