Considering the nature of marine accidents, even a single accident can result in significant damage to the environment and property, as well as loss of life. Therefore, the initial response should be rapid and accurate, and various decision support systems have been developed to achieve this. Research on simulating progressive flooding on board immediately after an accident is being actively conducted, but this requires high levels of computing power. In this study, a methodology for converting simulated ship motion data into a ship motion database is presented. The model of a training ship from the Korea Institute of Maritime and Fisheries Technology and KRISO in-house code SMTP was used for ship motion computations. The short-time Fourier transform was used to convert time-series motion data into a spectrogram motion database. A methodology for deriving a predicted location of the damage center is presented. The candidate locations of the damage centers were obtained by comparing the root mean square error values of the ship motion database from the simulation and real-time ship motion data. Finally, a probability function was suggested to confirm the predicted location of the damage center. Using 100 randomly selected test cases, our method showed 95% accuracy.