We perform first-principles calculations to study the high-order harmonic generation induced in graphene nanostructures by the laser field. Three distinct signals are noticed: the integer higher-order harmonic generation (HHG), the shifted fractional order peaks from the integer order harmonics, and the intrinsic emissions. Due to the small gap between HOMO and LUMO of graphene molecule, the HHG can be generated for the infrared laser pulse with the photon energy ranging from 20 meV to ∼1 eV. The intrinsic emission corresponds to the electron excitation between eigenstates. Using a laser pulse with a photon energy of 0.042 eV and amplitude of 0.2 V/Å, HHGs up to 19th order are identified. Unsaturated graphene molecule is an excellent medium for HHG. Moreover, the HHG signals are very sensitive to the hydrogen passivation. Our results also indicate that HHG can be a promising method for detecting the product in the fabrication of graphene molecules.