X-ray powder diffraction (XRD) was used to characterize and quantify nano-crystalline C-S-H in hydrated tricalcium silicate (C3S), Portland cement, and siliceous fly ash blended cement using Rietveld analysis with partial or no known crystal structure (PONKCS) coupled with thermalgravimetric analysis (TGA). Calibration of the C-SH profile was carried out by minimizing bound water content detected by TGA and XRD using least square minimization. Validation of the results was achieved by independent methods such as TGA and mass balance calculation. The PONKCS analysis provided acceptable accuracy of the C-S-H content. H2O content in C-S-H was derived based on the C-S-H content and bound water. Comparison of the extracted profile showed that the C-S-H crystallinity increased with an increase in Ca/Si atomic ratio. The full phase assemblage of the hydrated samples was obtained. Challenges in applying PONKCS method in C-S-H determination were discussed.