This study aims to elucidate the effect of heating on the local atomic arrangements, structure, phase transformation, and mechanical properties of synthesized calcium–silicate–hydrate (C–S–H). The alteration in the atomic arrangement of the synthesized C–S–H (Ca/Si =0.8) and the formation of crystalline phases that occurred in three distinct transformation stages of dehydration (105°C–200°C), decomposition (300°C–600°C), and recrystallization (700°C–1000°C) were investigated via powder X-ray diffraction, 29Si nuclear magnetic resonance spectroscopy, and thermogravimetric analysis. Further, the deformation of the local atomic bonding environment and variations in mechanical properties during the three stages were assessed via pair distribution function analysis based on in-situ total X-ray scattering. The results revealed that the C–S–H paste before heating exhibited a lower elastic modulus in real space than that in the reciprocal space in the initial loading stage because water molecules acted as a lubricant in the interlayer. At the dehydration stage, the strain as a function of external loading exhibited irregular deformation owing to the formation of additional pores induced by the evaporation of free moisture. At the decomposition stage, the structural deformation of the main d-spacing (d ≈ 3.0 Å) was similar to that of the real space before the propagation of microcracks. At the recrystallization stage, the elastic modulus increased to 48 GPa owing to the thermal phase transformation of C–S–H to crystalline β-wollastonite. The results provide direct experimental evidence of the microstructural and nanostructural deformation behavior of C–S–H pastes after exposure to high temperature under external loading.