Herein, the toughening mechanism and effects of 3-(aminopropyl)triethoxysilane (3-APTES) intercalation in calcium–silicate–hydrate (CSH) structures were investigated through molecular dynamics simulations. CSH established a model using 11 Å-tobermorite to simulate the tensile properties, toughness, adsorption energy, average orientation displacement and radial distribution function of 3-APTES intercalation at different Ca/Si ratios under conditions of a CVFF force field, an NVT system, and 298 K temperature. Simulation results demonstrate that 3-APTES alters the fracture process of CSH and effectively enhances its tensile properties and toughness. The presence of 3-APTES molecules increases the energy required to destroy CSH, thereby increasing the adsorption energy of CSH crystals. Furthermore, 3-APTES molecules effectively increase the atom density within the CSH structure. As the Ca/Si ratio increases, Ca–O bond formation is enhanced, with noticeable aggregation occurring because of modification by 3-APTES within the CSH structure. This study found that 3-APTES organic compounds can effectively improve the tensile, toughness, adsorption and other properties of the CSH structure, and further improve the microstructure of CSH.