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This invention relates to the fields of marine meteorology and navigation, and discloses a method for predicting meteorological factors for ship navigation based on marine meteorological information. This method is used to predict meteorological factors for ship navigation, assess navigation risks, and plan alternative routes. The method includes processing meteorological data and ship data for a target sea area to obtain historical meteorological time series and ship motion response sequences; constructing state vector trajectories of meteorological factors using historical meteorological data, establishing a dynamic model library, and obtaining the ship motion response function to meteorology based on meteorological and motion response data; generating deterministic meteorological factor prediction sequences by embedding the current meteorological state into the dynamic model; and constructing stochastic differential equations to generate probabilistic prediction distributions of meteorological factors. This invention integrates data-driven and physical constraints, providing more comprehensive navigation decision support.