Defects in graphene can profoundly impact its extraordinary properties, ultimately influencing the performances of graphene-based nanodevices. Methods to detect defects with atomic resolution in graphene can be technically demanding and involve complex sample preparations. An alternative approach is to observe the thermal vibration properties of the graphene sheet, which reflects defect information but in an implicit fashion. Machine learning, an emerging data-driven approach that offers solutions to learning hidden patterns from complex data, has been extensively applied in material design and discovery problems. In this paper, we propose a machine learning-based approach to detect graphene defects by discovering the hidden correlation between defect locations and thermal vibration features. Two prediction strategies are developed: an atom-based method which constructs data by atom indices, and a domain-based method which constructs data by domain discretization. Results show that while the atom-based method is capable of detecting a single-atom vacancy, the domain-based method can detect an unknown number of multiple vacancies up to atomic precision. Both methods can achieve approximately a 90% prediction accuracy on the reserved data for testing, indicating a promising extrapolation into unseen future graphene configurations. The proposed strategy offers promising solutions for the non-destructive evaluation of nanomaterials and accelerates new material discoveries.