To analyze the changing characteristics of ship traffic flow in wind farms water area, and to improve the accuracy of ship traffic flow prediction, a Gated Recurrent Unit (GRU) of a Recurrent Neural Network (RNN) was established to analyze multiple traffic flow sections in complex waters based on their traffic flow structure. Herein, we construct a spatiotemporal dependence feature matrix to predict ship traffic flow instead of the traditional ship traffic flow time series as the input of the neural network. The model was used to predict the ship traffic flow in the water area of wind farms in Yancheng city, Jiangsu Province. Autoregressive Integrated Moving Average (ARIMA), Support-Vector Machine (SVM) and Long Short-Term Memory (LSTM) were chosen as the control tests. The GRU method based on the spatiotemporal dependence is more accurate than the current mainstream ship traffic flow prediction methods. The results verify the reliability and validity of the GRU method.