Migratory corrosion inhibitors (MCIs) are regarded as effective additives to prevent harmful ion transmission and improve concrete durability, but their behavior in the porosity of concrete is still unclarified. This paper proposes a unique perspective to evaluate the effects of surfactant-like MCIs in calcium silicate hydrate (C-S-H) nanoporosity through molecular and electronic structural information. Advanced enhanced sampling methods and perturbation theory methods were applied to evaluate the role of different MCIs. The reduced density gradient of MCI molecules was obtained by using quantum chemical calculations. This calculation is instrumental in elucidating the intensity of interactions among distinct MCI molecule head groups and the C-S-H matrix. It is found that MCIs can effectively improve the interfacial tension (IFT) between C-S-H and water, which corresponds to the inhibitory ability of transmission. Free energy indicates that the MCI has the properties of strong adsorption and weak dissolution, facilitating the improvement of IFT. The relationship between the MCI functional group and the ability of adsorption and dissolution is revealed. This study suggests that MCIs work as surface controllers of C-S-H pores and that their properties can be assessed on the nanoscale.