Calcium silicate hydrate (C-S-H) is the most important component of cement hydration products, and is the main cementitious phase of cement-based materials. The interlayer water of C-S-H has a significant effect on its nanostructure and mechanical properties. The structure and mechanical properties of C-S-H with different humidity were studied by molecular dynamics method. The influence of humidity on the structure and elastic parameters of C-S-H as well as the mechanical and deformation properties under tension, compression and shear conditions were analyzed by radial distribution function and concentration distribution of atoms, elastic constants and stress-strain relationships. The results show that the increase of humidity leads more O atoms to accumulate around Si and Ca atoms in C-S-H, and makes the distance between layers larger and the stratification more obvious. At the same time, the increase of humidity also reduces the elastic properties of C-S-H. With the increase of humidity, the mechanical and deformation properties of C-S-H under different stress states reduce. The influence degrees on tensile strength and shear strength are greater than that on compressive strength. In terms of deformation properties, humidity has the greatest influence on deformation properties under tension and has the least influence on deformation properties under compression.