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Coupling of organic and inorganic chemistry presents a new degree of freedom in nano-engineering of thermo-mechanical properties of cement-based materials. Despite these vast technological benefits, molecular scale cross-linking of calcium-silicate-hydrate (C-S-H) gel with organic molecules still presents a significant challenge. Herein, we report experimental results on sol-gel synthesis, structure and morphology of nanocrystalline C-S-H cross-linked with dipodal organosilanes. These novel organic-inorganic gels have layered turbostratic molecular structure with similarities to C-S-H precipitating in hydrating cement paste. The organic molecules' chain length controls the interlayer spacing, which shows little to no shrinkage upon dehydration up to 105 °C. However, the structure gets distorted in the basal crystallite plane, in which dimer and trimer Si-polyhedra structures condense on a 2D hexagonal Ca-polyhedra layer. Cross-linked C-S-H gels display plate-like morphology with tendency toward stacking into agglomerates at the larger scale. If successfully realized in cement environment, e.g. high concentration seed, such novel organic-inorganic C-S-H gels could potentially provide cement-based matrices with unique properties unmatched by classical inorganic systems.