Short-term energy prediction plays an important role in green manufacturing in the industrial internet environment and has become the basis of energy wastage identification, energy-saving plans and energy-saving control. However, the short-term energy prediction of multiple nodes in manufacturing systems is still a challenging issue owing to the fuzzy material flow (spatial relationship) and the dynamic production rhythm (temporal relationship). To obtain the complex spatial and temporal relationships, a spatio-temporal deep learning network (STDLN) method is presented for the short-term energy consumption prediction of multiple nodes in manufacturing systems. The method combines a graph convolutional network (GCN) and a gated recurrent unit (GRU) and predicts the future energy consumption of multiple nodes based on prior knowledge of material flow and the historical energy consumption time series. The GCN is aimed at capturing spatial relationships, with the material flow represented by a topology model, and the GRU is aimed at capturing dynamic rhythm from the energy consumption time series. To evaluate the method presented, several experiments were performed on the power consumption dataset of an aluminum profile plant. The results show that the method presented can predict the energy consumption of multiple nodes simultaneously and achieve a higher performance than methods based on the GRU, GCN, support vector regression (SVR), etc.