Elastic materials are candidates for process intensification of gas storage by forming gas hydrate. In this work, molecular dynamics simulations of hydrate nucleation in elastic silica double layers were performed to study the effect of elastic confined spaces on hydrate formation. It is found that in narrow confined spaces, hexagonal rings dominated the hydrogen bond network of water molecules established rapidly by a multisite nucleation mechanism. With molecules added, a bilayer water structure was formed finally because elastic space can adapt the volume expansion. In medium and wide confined spaces, hydrates were formed from a series of "pseudo cages" which are considered as precursors of complete hydrate cages. Moreover, the induction time for nucleation was a minimum when the elasticity of the silica layer changes: nucleation is fastest in the weak-elastic system. When the elasticity increases, it becomes hard to adapt the volume expansion during nucleation and also difficult to nucleate in very weak-elastic systems because of the fluctuation of the layers.