To increase prediction accuracy of dissolved oxygen (DO) in aquaculture, a hybrid model based on multi-scale features using ensemble empirical mode decomposition (EEMD) is proposed. Firstly, original DO datasets are decomposed by EEMD and we get several components. Secondly, these components are used to reconstruct four terms including high frequency term, intermediate frequency term, low frequency term and trend term. Thirdly, according to the characteristics of high and intermediate frequency terms, which fluctuate violently, the least squares support vector machine (LSSVR) is used to predict the two terms. The fluctuation of low frequency term is gentle and periodic, so it can be modeled by BP neural network with an optimal mind evolutionary computation (MEC-BP). Then, the trend term is predicted using grey model (GM) because it is nearly linear. Finally, the prediction values of DO datasets are calculated by the sum of the forecasting values of all terms. The experimental results demonstrate that our hybrid model outperforms EEMD-ELM (extreme learning machine based on EEMD), EEMD-BP and MEC-BP models based on the mean absolute error (MAE), mean absolute percentage error (MAPE), mean square error (MSE) and root mean square error (RMSE). Our hybrid model is proven to be an effective approach to predict aquaculture DO.