Due to the limitation of graphene processing technology, the prepared graphene inevitably contains various defects. The defects will have a particular influence on the macroscopic characteristics of the graphene. In this paper, the defect-based graphene nanoresonators are studied. In this study, the resonant properties of graphene were investigated via molecular dynamic simulations. The effect of vacancy defects and hole defects at different positions, numbers, and concentrations on the resonance frequency of graphene nanoribbons was studied. The results indicated that single monatomic vacancy has no effect on graphene resonant frequency, and the concentration of the resonant frequency of graphene decreases almost linearly with the increase of single-atom vacancy concentration. When the vacancy concentration is 5%, the resonance frequency is reduced by 12.77% compared to the perfect graphene. Holes on the graphene cause the resonance frequency to decrease. As the circular hole defect is closer to the center of the graphene nanoribbon, not only does its resonant frequency increase, but the tuning range is also expanded accordingly. Under the external force of 10.715 nN, the resonant frequency of graphene reaches 429.57 GHz when the circular hole is located at the center of the graphene nanoribbon, which is 40 GHz lower than that of single vacancy defect graphene. When the circular hole is close to the fixed end of graphene, the resonant frequency is 379.62 GHz, which is 90 GHz lower than that of single vacancy graphene. When the hole defect is at the center of nanoribbon, the frequency tunable range of graphene reaches 120 GHz. The tunable frequency range of graphene is 100.12 GHz when the hole defect is near the fixed ends of the graphene nanoribbon. This work is of great significance for design and performance optimization of graphene-based nanoelectro-mechanical system (NEMS) resonators.