The construction of high-speed rail lines in China has drastically improved the freight capacity of conventional railways. However, due to recent national energy policy adjustments, rail freight volumes, consisting mostly of coal, ore, and other minerals, have declined. As a result, the corresponding changes in the supply and demand of goods and transportation have led to a gradual transformation of the railway freight market from a seller’s market to a buyer’s market. It is important to carry out a systematic analysis and a precise forecast of the demand for rail freight transport. However, traditional time series forecasting models often lack precision during drastic fluctuations in demand, while deep learning-based forecasting models may lack interpretability. This study combines grey relational analysis (GRA) and deep neural networks (DNN) to offer a more interpretable approach to predicting rail freight demand. GRA is used to obtain explanatory variables associated with railway freight demand, which improves the intelligibility of the DNN prediction. However, the high-dimension predictor variable can make training on DNN challenging. Inspired by deep autoencoders (DAE), we add a layer of an encoder to the GRA-DNN model to compress and aggregate the high-dimension input. Case studies conducted on Chinese railway freight from 2000 to 2018 show that the proven GRA-DAE-NN model is precise and easy to interpret. Comparative experiments with conventional prediction models ARIMA, SVR, FC-LSTM, DNN, FNN, and GRNN further validate the performance of the GRA-DAE-NN model. The prediction accuracy of the GRA-DAE-NN model is 97.79%, higher than that of other models. Among the main explanatory variables, coal, oil, grain production, railway locomotives, and vehicles have a significant impact on the railway freight demand trend. The ablation experiment verified that GRA has a significant effect on the selection of explanatory variables and on improving the accuracy of predictions. The method proposed in this study not only accurately predicts railway freight demand but also helps railway transportation companies to better understand the key factors influencing demand changes.