The invention discloses a mesoscale vortex trajectory prediction method. The method comprises the steps of downloading and reading satellite height measurement data, extracting mesoscale vortex characteristic parameters and position information, tracking mesoscale vortexes, establishing a mesoscale vortex trajectory prediction model based on a BP neural network, determining input and output data,training the BP neural network, and inputting the initial positions of the mesoscale vortexes into the trained prediction model for prediction. According to the invention, the BP neural network is used as a prediction model, and the tracked mesoscale vortex position information and the initial ground rotation flow velocity anomaly are used as model inputs, so that the short-term prediction of themesoscale vortex trajectory can be realized. Meanwhile, in the mesoscale vortex tracking process, the minimum distance method and the similarity method are combined, limitation on the mesoscale vortexamplitude is added, the error tracking rate is reduced, the tracking accuracy is guaranteed, and therefore the model prediction precision is improved.