Calcium silicate hydrate (C-S-H) is the main hydration product of cement, and its micro-nano-structure has an important influence on the properties of cement-based materials. The disadvantages of cement-based materials are related to the micro-nano-structure defects of C-S-H. The modification of the C-S-H structure by silane can make up the defects of C-S-H. Here, we studied the structure of C-S-H modified by a straight-chain silane containing silicon hydroxyl groups at both ends. Calcium silicate hydrate (C-S-H) gel particles modified by hydroxyl-terminated polydimethylsiloxane (PDMS) were synthesized by the sol–gel method. The influence of this organic modification on the structure of C-S-H was investigated by XRD, FTIR, NMR, SEM, TG-DTG and water contact angles techniques. The results show that various sizes of C-S-H gel particles are connected with PDMS via covalent bond. PDMS acts as a bridge between C-S-H particles. The introduction of PDMS changes the morphology of stacked spherical particles to cauliflower-like and increases water contact angle of C-S-H. In addition, various sizes of C-S-H gel particles are also coated by PDMS. This research explains the methods for affecting the stacking process of C-S-H gel particles.