The identification of atomic vacancy defects in graphene is an important and challenging issue, which involves inhomogeneous spatial randomness and requires high experimental conditions. In this paper, the fingerprints of resonant frequency for atomic vacancy defect identification are provided, based on the database of massive samples. Every possible atomic vacancy defect in the graphene lattice is considered and computed by the finite element model in sequence. Based on the sample database, the histograms of resonant frequency are provided to compare the probability density distributions and interval ranges. Furthermore, the implicit relationship between the locations of the atomic vacancy defects and the resonant frequencies of graphene is established. The fingerprint patterns are depicted by mapping the locations of atomic vacancy defects to the resonant frequency magnitudes. The geometrical characteristics of computed fingerprints are discussed to explore the feasibility of atomic vacancy defects identification. The work in this paper provides meaningful supplementary information for non-destructive defect detection and identification in nanomaterials.