The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans.