Chemical vapor deposition (CVD) is widely applied in synthesizing high quality graphene, whose size, shape and structure are strongly impacted by the hydrogen concentration and, however, its role is not fully understood. In the traditional CVD, the concentration of the hydrogen keeps the constant in whole synthesis process and subsequently the nucleation and growth process are carried out simultaneously, therefore, its roles are usually confused and indistinguishable. In this report, the role of hydrogen on the growth of graphene nanostructure was creatively studied by introducing a two-step method which divided the nucleation and growth process for the first time. In the first step, the hexagonal graphene domain grown with the same conditions was used as precursor to eliminate the impact of the nucleation. In the second step, the role of hydrogen on the growth of graphene nanostructure was investigated by controlling the hydrogen concentration. The evolution behavior of the graphene nanostructure with the hydrogen concentration was systematically investigated. Two roles of the hydrogen, namely growth and etching modes, are clearly disclosed and then a possible mechanism was proposed. The results shown here may provide valuable guidance to understand the graphene growth mechanism and further advance the synthesis of unique graphene nanostructure.