Restricted space could lead to the structure evolution of calcium silicate hydrate (C–S–H) especially during the later hydration stage, which essentially affects the strength and durability of Portland cement based materials. In order to get insights into the effect of restricted space on C–S–H microstructure, the alite powders were pressed into discs for hydration. The pre pressing treatment provides a relatively denser microstructure, which simulates the restricted space during the late hydration of alite or cement. The structure of hydrates grown in restricted space was revealed by Fourier transform infrared spectra, Raman spectra, 29Si nuclear magnetic resonance spectra, scanning electron microscope and energy dispersive X-ray spectroscopy. The results show that restricted space leads to the formation of unstable Ca–O bonds and Si–O bonds in early hydrates, and influences the silicate chains in C–S–H by the formation of high polymerized hydrates (Q3 silicates) at early stage. The content of Q3 silicates in the hydrates of restricted space is the highest at 7 d and then decreases, which is opposite to the control with the lowest Q3 silicates content at 7 d and the highest content at 28 d. The hydrates which form at 28 d show a remarkable higher chemical shift of Q3 sites and a lower Ca/Si ratio than that of the control. The findings indicate that the restricted space may lead to stress, which rearranges the nanostructure of C–S–H and induces a varied structure in Q3 silicates of C–S–H. This work lies a theoretical foundation for exploring the structure evolution of C–S–H in cement concrete after long service.