The mechanical properties of organic/inorganic composites can be highly dependent on the interfacial interactions. In this work, with organic polymers intercalated into the interlayer of inorganic calcium silicate hydrate (C-S-H), the primary binding phase of Portland cement, great ductility improvement is obtained for the nanocomposites. Employing reactive molecular dynamics, the simulation results indicate that strong interfacial interactions between the polymers and the substrate contribute greatly to strengthening the materials, when C-S-H/poly ethylene glycol (PEG), C-S-H/poly acrylic acid (PAA), and C-S-H/poly vinyl alcohol (PVA) were subject to uniaxial tension along different lattice directions. In the x and z direction tensile processes, the Si–O...Ca bonds of the C-S-H gel, which were elongated and broken to form Si–OH and Ca–OH, play a critical role in loading resistance, while the incorporation of polymers bridged the neighboring silicate sheets, and activated more the hydrolytic reactions at the interfaces to avoid strain localization, thus increasing the tensile strength and postponing the fracture. On the other hand, Si–O–Si bonds of C-S-H mainly take the load when tension was applied along the y direction. During the post-yield stage, rearrangements of silicate tetrahedra occurred to prevent rapid damage. The polymer intercalation further elongates this post-yield period by forming interfacial Si–O–C bonds, which promote rearrangements and improve the connectivity of the defective silicate morphology, significantly improving the ductility. Among the polymers, PEG exhibits the strongest interaction with C-S-H, and thus C-S-H/PEG possesses the highest ductility. We expect that the molecular-scale mechanisms interpreted here will shed new light on the stress-activated chemical interactions at the organic/inorganic interfaces, and help eliminate the brittleness of cement-based materials on a genetic level.