The problem of the benzene molecular structure has not been solved for a long time. This research proposes a new concept of covalent bonds based on the existing theory: each electron shared by the nucleus corresponds to a half-valent bond, and a half-valent bond can be formed between interval carbon atoms of the benzene ring. A new theory was established. Quantum mechanical calculations results can quantitatively explain experimental results, such as the hydrogenation heat and ultraviolet spectroscopy of benzene. It has solved more than one hundred years of difficult problems. The design of the new structural forms of benzene molecules shows half-valent bonds with dotted lines, which have a wide range of adaptability, and shows the structural forms and reaction formulas of more than dozens of benzene homologs and derivatives. Under the guidance of the new theory, the stacked three-dimensional structure of benzene was explored. The thickness of the three-layer benzene tube is calculated to be almost equal to the thickness of the graphene. Therefore, it is speculated that graphene may be a three layer structure.