The structure of calcium silicate hydrate ( C-S-H) gels was modified by hydrothermal reaction with aqueous acetic acid solvent, and then the C-S-H gels were used for dye removal from aqueous solution. With increasing acetic acid concentration, the Ca: Si molar ratio decreased and the length of the silicate anion chain structure of the C-S-H gels increased. The silicate anion chain length affects the number of available silanol groups on the surface of the C-S-H gel: the longer the silicate anion chain length, the greater the number of negative charges and the higher the surface potential. C-S-H gels with a long silicate anion structure exhibited higher adsorption capacity for methylene blue than gels with a short silicate anion structure. The enhanced adsorption capacity of the C-S-H gels is related to the higher number of silanol groups in the bridging silica tetrahedra of the intermediate anion chain structure compared with those in the end units of silica tetrahedra.