Soils and other geologic porous media often have contrasting grain size layers associated with a grain size transition zone between layers. However, this transition zone is generally simplified to a plane of zero thickness for modeling assumption, and its influence has always been neglected in previous studies. In this study, an approach combining a deposition process and a random packing process was developed to generate 3D porous media without and with consideration of the transition zone. The direct numerical models for solving the flow and concentration fields were implemented to investigate the influence of the grain size transition on flow and solute transport. Our results showed that although the transition zone occupied 13.6% of the entire layered porous medium, it had little influence on the distribution of flow velocity at the scale of the entire layered porous medium. However, the transition zone had a significant influence on the local flow field, which was associated with the increased spatial variability of velocity and the varied distribution of flow velocity. This varied local flow field could increase the solute residence time and delay the breakthrough time for solute transport. Although using both the advection-dispersion equation (ADE) and the mobile and immobile (MIM) models to fit the breakthrough curves (BTCs) for solute transport through layered porous media resulted in trivial errors, the ADE model failed to capture the influence induced by the local flow field, especially the influence of the transition zone. In contrast, the MIM model was shown to be able to capture the influence of the transition on solute transport. It was found that the mass transfer rate α, a parameter of the MIM model, was significantly improved by the presence of the transition zone, while it decreased as the transition zone fraction increased. Our study emphasized that the transition zone can vary the local flow field at the pore scale, while it has little influence on the hydraulic properties (e.g., hydraulic conductivity) of the macroscale flow field. However, the local flow field varied by the transition zone has a significant influence on solute transport.