In view of the importance of capillary pores to the physiomechanical properties of cement-based materials, it is essential to determine the volume fraction of capillary pores. The intention of this paper is to present a computer simulation-based method for predicting the volume fraction of capillary pores. By applying the periodic boundary conditions and introducing three physical parameters to quantify the mutual interference between neighboring cement particles, a computer simulation technique for the distribution and hydration of cement particles is described. Based on the simulated microstructure of cement paste, a numerical method is developed for the volume fraction of capillary pores. After verifying the numerical method with the experimental results obtained from the research literature, the effect of the water/cement ratio and the maximum cement diameter on the volume fraction of capillary pores is evaluated in a quantitative manner. It is found that, at a given hydration time, the volume fraction of capillary pores increases with the increase of the water/cement ratio and/or the maximum cement diameter. This paper concluded that the developed numerical method can predict the volume fraction of capillary pores with reasonable accuracy.