To more exactly predict the chloride diffusivity of cement paste, it is essential to determine the two-point probability function of capillary pores. The intention of the paper is to present a computer simulation method for evaluating the two-point probability function of capillary pores. By introducing three physical quantities to quantify the mutual interference between neighboring cement particles, the microstructure evolution of cement paste is simulated. Based on the simulated microstructure of cement paste, a numerical method is developed for evaluating the two-point probability function of capillary pores. After verifying the numerical method with the experimental results obtained from the literature, the effect of the hydration time and water/cement ratio on the two-point probability function is assessed in a quantitative manner. It is found that the two-point probability function decreases with the increase of the hydration time for a given water/cement ratio, but increases with an increase in water/cement ratio for a given hydration time.