Synthesis of calcium silicate hydrate (C-S-H) was conducted over the range of 50 degrees C-90 degrees C and C/S ratio of 0.86-2.14 in the highly alkaline Na2O-CaO-SiO2-H2O system for silicon utilization in high alumina fly ash. Structural change in C-S-H formed in the highly alkaline system was investigated using XRD and Si-29 MAS NMR spectra. X-ray photoelectron spectroscopy was used to confirm the amount of sodium ions in C-S-H. Conversion of Si may reach 99% under optimum conditions. A higher degree of polymerization of silicate was obtained at lower temperature and C/S ratio. Na+ was confirmed to exist as Na-OSi and Na-OH. The amount of Na+ is the least at C/S ratio of 1.43, which conform to the prediction of topological constraint theory. High Ca/Si ratio leads to the increasing in Na+ combined in the interlayer. Increasing in the Na+ concentration in the system also increases the amount of Na+ combined in the interlayer and reduces the polymerization. Ion exchange was proven to be an effective way to remove Na+ combined in the interlayer of C-S-H.