It has long been recognized, in cement chemistry, that two types of calcium-silicate-hydrate (C-S-H) exist in cement-based materials, but less is known about how the two types of C-S-H affect the mechanical properties. By means of nanoindentation tests on nondegraded and calcium leached cement paste, the paper confirms the existence of two types of C-S-H, and investigates the distinct role played by the two phases on the elastic properties of cement-based materials. It is found that (1) high-density C-S-H are mechanically less affected by calcium leaching than low density C-S-H, and (2) the volume fractions occupied by the two phases in the C-S-H matrix are not affected by calcium leaching. The nanoindentation results also provide quantitative evidence, suggesting that the elastic properties of the C-S-H phase are intrinsic material properties that do not depend on mix proportions of cement-based materials. The material properties and volume fractions are used in a novel two-step homogenization model, that predicts the macroscopic elastic properties of cement pastes with high accuracy. Combined with advanced physical chemistry models that allow, for a given w/c ratio, determination of the volume fractions of the two types of C-S-H, the model can be applied to any cement paste, with or without Portlandite, Clinker, and so on. In particular, from an application of the model to decalcified cement pastes, it is shown that that the decalcification of the C-S-H phase is the primary source of the macroscopic elastic modulus degradation, that dominates over the effect of the dissolution of Portlandite in cement-based material systems.