The understanding of microstructure and atomic arrangement in nanocrystalline phases with small particle sizes, below »50 Å, is intrinsically complicated. This challenge is exacerbated in samples with additional crystalline phase(s), like cement pastes. Here, we use synchrotron X-ray powder diffraction to quantitatively follow the tricalcium silicate hydration reactions. The dissolution of alite, an impure form of tricalcium silicate, as well portlandite crystallization and the calcium silicate hydrate (C-S-H) gel precipitation have been accurately measured by Rietveld methodology using an internal standard approach in unaltered pastes. Furthermore, synchrotron total scattering powder diffraction coupled to pair distribution function (PDF) methodology has been used to characterize the alite hydration products. We have used a multi r-range analysis approach, where the 40–70 Å r-interval allows determining the crystalline phase contents; the 10–25 Å r-range is used to get information about the atomic ordering in the nanocrystalline component; and the 2–10 Å region gives insights about the amorphous component. Specifically, a defective clinotobermorite, Ca₁₁Si₉O₂₈(OH)₂^.8.5H₂O with density »2.5 gcm^-3, gave the best PDF fit for a carefully-prepared hydrated alite sample. Furthermore, the PDF analysis also indicates that C-S-H gel is mainly composed of this defective tobermorite and monolayer calcium hydroxide which is stretched as recently predicted by first principles calculations. Chiefly, these outcomes together with nuclear magnetic resonance data, electron microscopy results and previous reports yielded a multiscale picture for C-S-H gel nanocomposite which help to explain the observed densities and Ca/Si atomic ratios at the nano- and meso- scales.