When two two-dimensional (2D) materials with different lattice constants or with different rotation angles are superimposed, a moiré superlattice can be constructed. The electronic properties of the superlattice are strongly dependent on the stacking configuration, twist angle and substrate. For instance, theoretically, when the rotation angle of twisted bilayer graphene is reduced to a set of specific values, the so-called magic angles, flat bands appear near the charge neutrality, and the electron-electron interaction is significantly enhanced. The Mott insulator and unconventional superconductivity are detected in the twisted bilayer graphene with a twist angle around 1.1°. For a moiré pattern with a large enough periodicity, lattice relaxation caused by an interplay between van der Waals force and the in-plane elasticity force comes into being. The atomic relaxation forces atoms to deviate from their equilibrium positions, and thus making the system reconstructed. This review mainly focuses on the effects of the lattice relaxation and substrates on the electronic properties of the graphene superlattices. From both theoretical and experimental point of view, the lattice relaxation effects on the atomic structure and electronic properties of graphene-based superlattices, for example, the twisted bilayer graphene, twisted trilayer graphene, graphene-hexagonal boron nitride superlattice and twisted bilayer graphene-boron nitride superlattice are discussed. Finally, a summary and perspective of the investigation of the 2D material superlattice are presented.