Abstract A variety of submesoscale coherent vortices (SCVs) in the Kuroshio Extension region have been reported by recent observational studies, and the preliminary understanding of their properties, spatial distribution, and possible origins has progressively improved. However, due to relatively sparse in situ observations, the generation mechanisms of these SCVs and associated dynamic processes remain unclear. In this study, we use high-resolution model simulations to fill the gaps of the in situ observations in terms of the three-dimensional structures and life cycles of SCVs. Vortex detection and tracking algorithms are adopted and the characteristics of warm-core and cold-core SCVs are revealed. These vortices have finite Rossby numbers (0.25–0.4), and their horizontal structures can be well described by the Taylor vortex model in terms of the gradient wind balance. The vertical velocity field is characterized by a distinct dipole pattern with upwelling and downwelling cells at the vortex edge. It is very likely that both types of SCVs are generated along the eastern Japan coast through flow–topography interactions, and the Izu–Ogasawara Ridge and Hokkaido slope are found to be two important generation sites where topography friction produces extremely low potential vorticity. After leaving the boundary, SCVs can propagate over long distances and trap a water volume of ∼1011 m3.