Properties of organic/inorganic composites can be highly dependent on the interfacial connections. In this work, molecular dynamics, using pair-potential–based force fields, was employed to investigate the structure, dynamics, and stability of interfacial connections between calcium–silicate–hydrates (C–S–H) and organic functional groups of three different polymer species. The calculation results suggest that the affinity between C–S–H and polymers is influenced by the polarity of the functional groups and the diffusivity and aggregation tendency of the polymers. In the interfaces, the calcium counterions from C–S–H act as the coordination atoms in bridging the double-bonded oxygen atoms in the carboxyl groups (−COOH), and the Ca–O connection plays a dominant role in binding poly(acrylic acid) (PAA) due to the high bond strength defined by time-correlated function. The defective calcium–silicate chains provide significant numbers of nonbridging oxygen sites to accept H-bonds from −COOH groups. As compared with PAA, the interfacial interactions are much weaker between C–S–H and poly(vinyl alcohol) (PVA) or poly(ethylene glycol) (PEG). Predominate percentage of the −OH groups in the PVA form H-bonds with inter- and intramolecule, which results in the polymer intertwining and reduces the probability of H-bond connections between PVA and C–S–H. On the other hand, the inert functional groups (C–O–C) in poly(ethylene glycol) (PEG) make this polymer exhibit unfolded configurations and move freely with little restrictions. The interaction mechanisms interpreted in this organic–inorganic interface can give fundamental insights into the polymer modification of C–S–H and further implications to improving cement-based materials from the genetic level.