The dry and wet cyclic crystallization of sodium chloride (NaCl) can damage cement concrete materials, and the limitations of the existing experimental methods make it difficult to study the salt crystallization damage mechanism from the nanoscale. Therefore, this paper adopted the molecular dynamics method for the main microscopic product of cement hydration, calcium silicate hydrate (C-S-H) gel, to study the evaporation crystallization process of NaCl in the amorphous pores of C-S-H gel and the crystallization damage mechanism. The results show that the C-S-H gel amorphous model constructed in this paper is closer to the C-S-H gel with low density, and the evaporation crystallization of NaCl in the pores of this model follows a two-step nucleation mechanism, and the filling of C-S-H gel nanopores by evaporated crystallized NaCl crystals significantly reduces the overall tensile deformation capacity of C-S-H gel, and makes C-S-H gel brittle, which is a conclusion to this conclusion provides a basis for explaining the phenomenon of C-S-H gel destruction under the action of evaporation crystallization.