Using first-principles density functional theory calculations, two types of junction models constructed from armchair and zigzag carbon nanotube (CNT) insertion into a graphene matrix have been envisioned. It has been found that the insertion of the CNT into the graphene matrix leads to the formation of C–C covalent bonds between graphene and the CNT that distort the CNT geometry. However, the hydrogenation of the suspended carbon bonds on the graphene resumes the graphene-like structure of the pristine tube. The calculated band structure of armchair CNT insertion into graphene or hydrogenation graphene opens up a band gap and converts the metallic CNT into a semiconductor. For the zigzag CNT, the sp3 hybridization between the graphene and nanotube alters the band structure of the tube significantly, whereas saturating the dangling bonds of terminal carbon atoms of graphene makes the CNT almost keep the same character of the bands as that in the pristine tube. The synthesis of our designed hybrid structures must be increasingly driven by an interest in molecules that not only have intriguing structures but also have special functions such as hydrogen storage.