Short-term traffic volume prediction, which can assist road users in choosing appropriate routes and reducing travel time cost, is a significant topic of intelligent transportation system. To overcome the error magnification phenomena of traditional combination methods and to improve prediction performance, this paper proposes an improved Bayesian combination model with deep learning (IBCM-DL) for traffic flow prediction. First, an IBCM framework is established based on the new BCM framework proposed by Wang. Then, correlation analysis is used to analyze the relevance between the historical traffic flow and the traffic flow within the current interval. Three sub-predictors including the gated recurrent unit neural network (GRUNN), autoregressive integrated moving average (ARIMA), and radial basis function neural network (RBFNN) are incorporated into the IBCM framework to take advantage of each method. The real-world traffic volume data captured by microwave sensors located on the expressways of Beijing was used to validate the proposed model in multiple scenarios. The overall results illustrate that the IBCM-DL model outperforms the other state-of-the-art methods in terms of accuracy and stability.