Nitrogen-doped graphene potentially could be used in electronic devices, sensors, and energy-based devices. The bonding state between the carbon and nitrogen for each application plays an important role, e.g., the graphitic nitrogen has a high catalytic activity in fuel cell systems. However, it is still difficult to synthesize the bonding state selectivity. We conducted a nitrogen neutral beam modification of graphene, which has precise controllable beam energy. XPS analysis revealed that the bonding state of the carbon nitrogen depends on the beam energy and a moderate level of beam energy from a nitrogen neutral beam selectively forms graphitic carbon. The bonding state control during the nitrogen doping process was found to be possible, and a neutral beam induced doped graphene synthesis could potentially be better for many different applications.