Cementitious composites are ubiquitous in infrastructure, but their durability is often limited by interfacial weaknesses, particularly when bonded to epoxy polymers. These organic-inorganic interfaces are critical in applications such as fiber-reinforced polymer repair, strengthening, and additive concrete manufacturing. However, debonding and cracking at the epoxy-calcium silicate hydrate (CSH) interface under conditions such as elevated temperature, moisture, or fatigue-loading remain long-standing challenges. A fundamental understanding of the atomic-level interactions governing macroscopic interfacial properties is essential to optimize the performance of these composites; however, these remain largely unexplored by conventional analytical techniques owing to the buried nature of the nanoscale epoxy-CSH interface. In this study, we employed classical molecular dynamics (MD) simulations to elucidate the molecular mechanisms associated with epoxy-modifier-incorporated (nanofillers-incorporated) epoxy prepolymer (i.e., liquid epoxy) adsorption, wetting, and adhesion to CSH surfaces. We investigated three epoxy systems: epoxy prepolymer, acrylamide-modified (AM-modified) epoxy prepolymer, and nanosilica-reinforced (nano-SiO₂-reinforced) epoxy prepolymer, with their pre-curing interactions with CSH simulated for the first time. Key interfacial parameters, including interphase formation, wetting ratio, atomic-density profile, monomer-concentration profile, interfacial ionic and hydrogen bonding, interaction energy, and work of adhesion, were rigorously analyzed. Our MD simulations revealed that the diethyltoluenediamine (DETDA) epoxy hardener preferentially adsorbs over bisphenol F diglycidyl ether (DGEBF) resin on the CSH surface, leading to a hardener-rich interphase. Both resin and hardener components were found to concentrate within approximately 5 Å of the CSH surface and exhibit molar ratios significantly higher than that of the bulk, suggestive of a potentially stiffer interphase. The incorporation of AM was found to significantly enhance interfacial adhesion and improve adsorption and wetting through strong electrostatic and hydrogen bonding, resulting in a 16.43% increase in the work of adhesion compared to neat epoxy. The nanosilica filler, while improving interfacial interactions, aggregated and yielded a modest enhancement of 4.45% in the work of adhesion. These findings provide fundamental and novel molecular-level insights for the rational design of epoxy-modified cementitious composites with enhanced interfacial-bonding, durability, and mechanical properties. This study underscores the critical role played by nanofiller selection in tailoring interfacial properties and offers valuable guidelines for material formulations that optimize the interphase region in high-performance polymer-cement hybrid materials.