Water transportation today has become increasingly busy because of economic globalization. In order to solve the problem of inaccurate port traffic flow prediction, this paper proposes an algorithm based on gated recurrent units (GRUs) and Markov residual correction to pass a fixed cross-section. To analyze the traffic flow of ships, the statistical method of ship traffic flow based on the automatic identification system (AIS) is introduced. And a model is put forward for predicting the ship flow. According to the basic principle of cyclic neural networks, the law of ship traffic flow in the channel is explored in the time series. Experiments have been performed using a large number of AIS data in the waters near Xiazhimen in Zhoushan, Ningbo, and the results show that the accuracy of the GRU-Markov algorithm is higher than that of other algorithms, prov-ing the practicability and effectiveness of this method in ship flow prediction.