With the rapid development of China’s civil aviation, the flow of air traffic in terminal areas is also increasing. Short-term air traffic flow prediction is of great significance for the accurate implementation of air traffic flow management. To enhance the accuracy of short-term air traffic flow prediction, this paper proposes a short-term air traffic flow prediction model based on complementary ensemble empirical mode decomposition (CEEMD) and long short-term memory (LSTM) of the Bayesian optimization algorithm and data differential processing. Initially, the model performs CEEMD on the short-term air traffic flow series. Subsequently, to improve prediction accuracy, the data differencing is employed to stabilize the time series. Finally, the smoothed sequences are, respectively, input into the LSTM network model optimized by the Bayesian optimization algorithm for prediction. After data reconstruction, the final short-term flow prediction result is obtained. The model proposed in this paper is verified by using the data from Shanghai Pudong International Airport. The results show that the evaluation indexes of the prediction accuracy and fitting degree of the model, RMSE (Root Mean Square Error), MAE (Mean Absolute Error), and R2 (Coefficient of Determination), are 0.336, 0.239, and 97.535%, respectively. Compared to other classical time-series prediction models, the prediction accuracy is greatly improved, which can provide a useful reference for short-term air traffic flow prediction.