The Kuroshio Extension (KE) region is the key area in mid-latitude ocean-atmosphere interaction where mesoscale eddies achieve their largest activity. The eddy-mean flow interaction here plays a critical role in Kuroshio meander dynamics. In the past, most researchers focused on the individual cases of mesoscale eddies, or eddies in sea surface using the satellite observations. In recent years, by applying the composite analysis of multiple data (such as satellite altimetry, Argo float data, mooring data), some universal eddy structures were proposed. However, the vertical structure of eddy energy is seldom emphasized. Adopting an automated eddy detection scheme to the OFES (OGCM for the Earth Simulator) high-resolution eddy resolving ocean simulation product during the period of 1990-1997, a three-dimensional eddy data set in KE region is developed. It includes information for 82080 individual eddies’ location, polarity, intensity, size, boundary, and trajectory at 54 vertical levels. Based on this data set, we analyze the vertical structure of eddy energy by calculating the energy budget during the generation, evolution and termination of the eddies’ life. We raise universal eddy energy vertical structures for cyclonic and anticyclonic eddies during the mean flow-eddy interaction processes. These findings are significant for a better understanding of the mechanism for the vertical structure of mesoscale eddies and the mean flow-eddy interaction processes.