In the application of Bayesian networks to solve practical problems, it is likely to encounter the situation that the data set is expensive and difficult to obtain in large quantities and the small data set is easy to cause the inaccuracy of Bayesian network (BN) scoring functions, which affects the BN optimization results. Therefore, how to better learn Bayesian network structures under a small data set is an important problem we need to pay attention to and solve. This paper introduces the idea of parallel ensemble learning and proposes a new hybrid Bayesian network structure learning algorithm. The algorithm adopts the elite-based structure learner using genetic algorithm (ESL-GA) as the base learner. Firstly, the adjacency matrices of the network structures learned by ESL-GA are weighted and averaged. Then, according to the preset threshold, the edges between variables with weak dependence are filtered to obtain a fusion matrix. Finally, the fusion matrix is modified as the adjacency matrix of the integrated Bayesian network so as to obtain the final Bayesian network structure. Comparative experiments on the standard Bayesian network data sets show that the accuracy and reliability of the proposed algorithm are significantly better than other algorithms.