Eddy vertical structure is crucial for estimating the eddy-induced mass, energy, heat and salt flux. By combination of the satellite altimeter data and Argo profile data, an eddy vertical structure reconstruction method based on dynamics theory is devised. Different from the previous eddy composite method, this method considers the impact of the background and eddy-induced sea surface height anomaly on the thermohaline structure of eddy interior, and normalizes the eddy amplitude based on the quasi-geostrophic theory. Then it is applied on the study of eddies in the eastern boundary of the southern Indian Ocean. Results show that anti-cyclonic eddies (AEs) in this region are commonly surface intensified, which only influence a shallow depth (<500m). The density and temperature core of the regional characteristic AE are, respectively, at depth of 120 m with a density anomaly of -0.49 kg/m³ and 270 m with a temperature anomaly of 1.75 ℃. The geostrophic current velocity of the AE decreases rapidly with increasing depth and it is only 20% of the surface level at depth of 360 m. However, cyclonic eddies (CEs) are subsurface intensified and can penetrate for a very deep depth (>1500 m). The density and temperature core of the regional characteristic CE are, respectively, at depth of 650 m with a density anomaly of 0.24 kg/m³ and 630 m with a temperature anomaly of -2.31 ℃. The geostrophic current velocity of the AE as a function of depth show an S-shape structure with a maximum speed at depth of about 200m.