Calcium silicate hydrate (C-S-H) gels shrink upon drying and swell upon on wetting due to the specific water sensitivity, making that the pore structure of cement-based material depends on its water content. The representativeness and accuracy of the pore structure characteristics and its development obtained in a totally dry state are questionable because of the influence of drying preconditioning. To explore the evolution of pore structure of cement-based materials with respect to water to cement (w/c) ratio, several typical white cement mortars were investigated by low-field nuclear magnetic resonance (LF-NMR) and mercury intrusion porosimetry (MIP). Meanwhile, their permeability coefficients to water were also measured. The results show that the discrete pore size distribution (PSD) achieved by LF-NMR in a water-saturated state can be used to predict the water permeability through a classical Kozeny-Carman model based on the parallel cylindrical pores. The effect of w/c ratio on the pore structure of water-saturated mortars is consistent with that on the water permeability. However, the PSD curves measured by MIP scatter remarkably, which cannot reflect the effect of w/c ratio on the pore structure of mortars. As a result, the pore structural characteristics obtained in a dry state are limited, which makes the typical pore classifications questionable. Since the pore structure plays a fundamental role in interpreting almost all the properties of hardened cement-based materials, it is essential to detect the more relevant pore structure in a water-saturated state through LF-NMR to avoid the effect of drying preparation.