A new approach for scalable synthesis of three-dimensional graphene (3d-G) with the assistant of silica is reported. Silica is generated on the surface of graphene oxide through a facile solution reaction. Graphene coated by silica is reduced through thermal reduction. 3d-G can be obtained after the subsequent etching process. The structures and morphologies of samples are investigated. It is demonstrated that the agglomeration of individual graphene sheets during the thermal reduction is effectively avoided under the perfect protection of silica. The electrochemical studies of the material show a significant enhancement in the specific capacity and rate capability of the lithium ion battery over commercially available graphite electrodes due to its unique 3D cross-linked graphene architecture. This method enables us to develop a facile and effective approach to scalable preparation of graphene.