Dissolved oxygen is an important environmental factor for prawn breeding. In order to improve the prediction accuracy of dissolved oxygen concentration in prawn pond, and solve the problem of low prediction accuracy of different frequency domain modal classification after empirical modal decomposition of nonlinear time series data when there are few training samples, an combination prediction model based on empirical mode decomposition (EMD), random forest (RF) and long short term memory neural network (LSTM) was proposed in this research. Firstly, the time series data of prawn breeding dissolved oxygen concentration were decomposed at multiple scales by EMD to obtain a set of stationary intrinsic mode function (IMF). Secondly, with fewer training samples, poor predicts effects on the low-frequency were verified component by LSTM. Then, IMF1－IMF4 were divided into high-frequency components through test results and used for LSTM model. IMF5－IMF7, Rn were divided for RF model, the EMD-RF-LSTM combination model was constructed to improve the prediction accuracy. Modeled low-frequency and high-frequency components IMF using RF and LSTM, then predictions of each component were accumulated and the prediction value of dissolved oxygen of sequence data were got. Finally, the performance of the model was compared with the limit learning machine (ELM), RF, standard LSTM, EMD-ELM and EMD-RF, EMD-LSTM, etc. In the test based on real dataset, the EMD-ELM model contrasted with ELM model, reduced the mean absolute error (MAPE), root mean square error (RMSE) and mean absolute error (MAE) by 30.11%, 29.60% and 32.95%, respectively. The MAPE, RMSE, MAE for the proposed models were 0.0129,0.1156,0.0844, respectively. MAPE decreased by 84.07%, 57.57%, and 49.81% compared with EMD-ELM, EMD-RF and EMD-LSTM, respectively, the prediction accuracy was significantly improved. The results show that the proposed model EMD-RF-LSTM has good prediction performance and generalization ability, which is meets the actual demand of accurate prediction of dissolved oxygen concentration in prawn culture, and can provide reference for the prediction and early warning of prawn pond water quality.