Due to the unique structure and excellent physicochemical properties, ionic liquids have shown a broad application prospect. However, some water inevitably exists in ionic liquids during applications. The presence of waters has a significant impact on the structure and properties of ionic liquids. In this work, the microstructure, interactions and transport properties of [Bmim][B(CN)4], [Bmim][PF6] and [Bmim][Tf2N] with different contents of water were systematically studied by molecular dynamics simulations. By analyzing the number of hydrogen bonds for the system of ionic liquids and water, it was found that the number of hydrogen bonds between anions and water increased significantly with increasing water content, while the number of hydrogen bonds between anions and cation decreased gradually with the increase of water content. The number of hydrogen bonds between anions and water were greater than those between cations and water. The self-diffusion coefficients for the mixture of ionic liquids and water were calculated. It was found that the self-diffusion coefficient of the ionic liquid increased gradually with the increase of the water content. The more hydrophilic the ionic liquids were, the more the diffusion coefficient increased. The radial distribution function and coordination number results showed that the interaction between anions and water was stronger than that between cations and water. However, addition of water to ionic liquids was found to have no impact on the structure between anions and cations. In addition, the results of the spatial distribution function suggested that the distribution of anions and water around H5 and H4 of imidazolium cation ring were competitive, which reduced the interaction between cations and anions. This research results can help to further understand the microscopic mechanism of ionic liquids and water system and promote the application of ionic liquids.