In this study, the pore structure of Portland cement paste is experimentally characterized by MIP (mercury intrusion porosimetry) and nitrogen adsorption, and simulated by a newly developed status-oriented computer model. Cement pastes with w/c=0.3, 0.4 and 0.5 at ages from 1 day to 120 days are comprehensively investigated. It is found that MIP cannot generate valid pore size distribution curves for cement paste. Nevertheless, nitrogen adsorption can give much more realistic pore size distribution curves of small capillary pores, and these curves follow the same distribution mode. While, large capillary pores can be effectively characterized by the newly developed computer model, and the validity of this model has been proved by BSE imaging plus image analysis. Based on the experimental findings and numerical simulation, a hypothesis is proposed to explain the formation mechanism of the capillary pore system, and the realistic representation of the pore structure of hydrated cement paste is established.