Exploring and modifying the C-S-H structure at a micro–nano level is an effective solution to improve the performance of Portland cement. Compared with organics inserting C-S-H, the research on the performance of a polymer-binding C-S-H structure from nanoscale to macroscale is limited. In this work, the mechanical properties of a modified C-S-H, using hydroxyl-terminated polydimethylsiloxane (PDMS) as the binders, are evaluated. The PDMS-modified C-S-H structures are introduced into macro-defect-free cement to obtain stress–strain curves changes at a macro scale. The AFM–FM was adopted to measure the morphology and elastic modulus of C-S-H at a nano scale. The molecular dynamics (MD) simulation was performed to assess the toughness, tensile properties, and failure mechanism. The results show that the PDMS-modified C-S-H powders change the break process and enhance ductility of MDF cement. The elastic modulus of PDMS-modified C-S-H is lower than pure C-S-H. When PDMS molecules are located between the stacking crystal units, it can enhance the toughness of C-S-H aggregates. The PDMS-modified C-S-H stacking structure has better plasticity, and its tensile strains are higher than the pure C-S-H. PDMS molecules hinder the initial crack expansion, leading to the branching of the initial crack. In addition, the measurement of AFM–FM can identify and obtain the mechanical properties of basic units of C-S-H. This paper enhances the understanding of cement strength sources and modification methods.