The combination of vertical and in-plane heterostructures will create unprecedented structures that may produce novel physical properties. In this study, the failure mechanism of a bilayer Gr/h-BN staggered stacked heterostructure (BGBN-SS) with different interlayer sp3 bonds, different interface connection, and various defects has been investigated. The results show that interlayer sp3 bonds and various defect affect the failure mechanism of BGBN-SS in two contrary ways. The sp3 bonds raise the primary strain of the BGBN-SS-containing various defects and different interface connection, and can weaken tensile stresses and strain and Young’s modulus. However, the creation of interlayer bonding leads the bilayer heterostructure gradually changed to “quasi three-dimensional” structure. The stronger interlayer interaction induced by sp2–sp3 bonds in “quasi three-dimensional” structure can strengthen the interlayer shell modulus and load transfer rate. In addition, the mechanical properties of interface C–N bonding are greater than that of interface C–B bonding, indicating that C–N bonding at interface could improve the stability and ductility of the composite effectively. The square nanoholes are more likely to accumulate the local stress of the system, compared with circular nanoholes. The changing of sp2 hybridization of interlayer bonds transforms to a weak hybrid sp3 bonds. As a result, the special defects (interlayer bonding) introduce a new stress transfer mode (different from vdW heterostructures and in-plane hybrid nanostructures.