Calcium silicate hydrate is the primary hydration product of Portland cement and plays a crucial role in determining the strength of cement-based materials. The structural and dynamic properties of water molecules within calcium silicate hydrate nanopores have significant implications for the mechanical and durability performance of these materials. However, the influences of pore size and temperature on the properties of water molecules have not been fully explored. In this work, using molecular dynamics simulations and theoretical analysis, the evolution and mechanisms of the structural and dynamic properties of water molecules in different scenarios with various pore sizes and temperatures are systematically investigated. It is shown that the diffusion coefficients of water molecules increase with both pore size and temperature. Moreover, water molecules have a tendency to adsorb onto calcium silicate hydrate substrates, forming a distinct layered structure. As a result, the water molecules near the surfaces of calcium silicate hydrate substrates exhibit limited mobility, leading to smaller diffusion coefficients compared to those in other regions. Additionally, the distinctions in properties between water molecules and Ca²⁺ ions are elucidated and the underlying mechanisms behind these differences are also unveiled. The results and findings in this work deepen the understanding of structural and dynamic properties of water molecules within calcium silicate hydrate nanopores, providing valuable insights for improving the mechanical and durability performance of cement-based materials.