In turbomachinery, strongly unsteady rotor–stator interaction triggers complex three-dimensional turbulent flow phenomena such as flow separation and vortex dynamics. Large eddy simulation (LES) is an advanced numerical method that has recently been used to resolve large-scale turbulent motions and model subgrid-scale turbulence in turbomachinery. To largely reduce the computing cost of LES for turbomachinery flow, a graphics processing unit (GPU)-accelerated deep neural network-based flow field prediction approach is explored, which combines convolutional neural network autoencoder (CNN-AE) with long short-term memory (LSTM). CNN-AE extracts spatial features of turbomachinery flow by mapping high-dimensional flow fields into low-dimensional space, while LSTM is used to predict the temporal evolution of fluid dynamics. Automatic mixed precision (AMP) is employed to achieve rapid neural network training using Nvidia GTX 1080 Ti GPU, which shows a significant speedup compared with that without AMP. We evaluated the proposed CNN-AE-LSTM (CAL) method against gated recurrent units (GRU) and simple recurrent network (SRN) on two types of turbomachinery, i.e., centrifugal and axial flow pumps. The results show that the proposed CAL shows better capability of capturing the vortex structure details of turbomachinery. When predicting the temporal vorticity field, the mean square error of CAL results is 0.105%–0.124% for centrifugal pumps and 0.071%–0.072% for axial flow pumps. Meanwhile, the structural similarity index measure of the CAL results is 92.51%–92.77% for centrifugal pumps and 93.81%–94.61% for axial flow pumps. The proposed CAL is noticeably better than GRU and SRN in terms of both mean square error and structural similarity index measure.