The combination of graphene (Gr) and graphene-like materials provides the possibility of using two-dimensional (2D) atomic layer building blocks to create unprecedented architectures. The most attractive characteristics are strongly dependent on the various spatial structures, mainly including in-plane heterostructures butt-joined at the side of an atomic monolayer through covalent bonds, van der Waals (vdW) heterostructures involving a vertically stacked hybrid structure, and their combinations. Heterostructures can not only overcome the limitations inherent to each material but may also obtain new features by appropriate material combination. However, heterostructures made of vdW force superposition or covalent bond splicing are prone to defects. The introduction of external and internal defects causes local deformation and stress in the material, thereby affecting the physical properties of the material, such as its transport properties and mechanical properties. Therefore, research, utilization and control of these defects are highly critical. This paper reviews the vacancy, topological and geometrical effects of defects in modulating the structures and mechanical responses of Gr-based heterostructures. Moreover, the coupling effects of various defects on the Gr-based heterostructures in multi-physics fields are also discussed. This work aims to improve the understanding of the physical mechanism of defective configurations and their association in low dimensions, so as to realize various configurations and to aid the search for new usages.