Although the calcium silicate hydrate (C-S-H) has been used for millennium, the structure and formation of C-S-H are still unclear at atomistic level. In this work, we find two kinds of calcium silicate aqua complexes, [Ca(HO)(SiO(OH))] and [Ca(HO)(SiO(OH))], prior to the nuleation of C-S-H. The ab initio metadynamics simulations show that [Ca(HO)(SiO(OH))] and [Ca(HO)(SiO(OH))] have six and five stable states on the free energy surface (FES), respectively. There are different ligand substitution mechanisms between the FES minima. The four- and six- coordinated [Ca(HO)(SiO(OH))] only follow associative and dissociative mechanisms, respectively. While both dissociative and associative mechanisms apply to the six-coordinated [Ca(HO)(SiO(OH))] and no four-coordinated ligand substitution reaction is found. The most stable states in both systems show a distorted Ca[sbnd]O octahedral feature. Our findings may promote a fundamental understanding for the calcium silicate based species in solution and pre-nucleation process of C-S-H.