The vertical structure of eddies in the Leeuwin Current system affects the eddy volume, heat, and salt transport, even the ecosystem. However, the understanding of eddy vertical structure and eddy-induced transport here are still very limited. In this study, satellite observed sea surface heights were combined with decade-long in situ measurements of Argo floats to study the vertical structure of mesoscale eddies in the LC system and their volume, heat, and salt transport. A novel eddy reconstruction method, which considers the influences of both the eddy and background flow, is devised to study the three-dimensional structure of eddies. Result shows that, in LC system, anticyclonic eddies (AEs) are usually surface-intensified, with the geostrophic velocity decreasing sharply below the mixed layer, while cyclonic eddies (CEs) are subsurface-intensified, with a maximum speed at 240 m. The density anomaly core of the average AE (CE) is at a depth of 130 m (650 m) with a density anomaly of −0.51 (0.24) kg/m³. The volume-integrated eddy kinetic energy and available potential energy of the average CE are much larger than those of the average AE. The average lifespan of CEs is significantly longer than that of AEs, which can be explained by the deeper vertical scale of CEs. The offshore volume transport by eddy drift across the coastal (107°E) section is 9.05 Sv (12.5 Sv). The heat and salt onshore transport by eddy drift across the coastal (107°E) section are, respectively, 10.6 Tw and 143.1 ton/s (17.1 Tw and 241.0 ton/s).