Precise time series prediction serves as an important role in constructing a Digital Twin (DT). The various internal and external interferences result in highly non-linear and stochastic time series data sampled from real situations. Although artificial Neural Networks (ANNs) are often used to forecast time series for their strong self-learning and nonlinear fitting capabilities, it is a challenging and time-consuming task to obtain the optimal ANN architecture. This paper proposes a hybrid time series prediction model based on ensemble empirical mode decomposition (EEMD), long short-term memory (LSTM) neural networks, and Bayesian optimization (BO). To improve the predictability of stochastic and nonstationary time series, the EEMD method is implemented to decompose the original time series into several components, each of which is composed of single-frequency and stationary signal, and a residual signal. The decomposed signals are used to train the BO-LSTM neural networks, in which the hyper-parameters of the LSTM neural networks are fine-tuned by the BO algorithm. The following time series data are predicted by summating all the predictions of the decomposed signals based on the trained neural networks. To evaluate the performance of the proposed hybrid method (EEMD-BO-LSTM), this paper conducts a case study of wind speed time series prediction and has a comprehensive comparison between the proposed method and other approaches including the persistence model, ARIMA, LSTM neural networks, B0-LSTM neural networks, and EEMD-LSTM neural networks. Results show an improved prediction accuracy using the EEMD-BO-LSTM method by multiple accuracy metrics.