Abstract Electron-scale magnetic holes filled with high-energy electrons can provide a seed population of electrons in the magnetosphere and might play an important role in the interaction between the magnetosphere and solar wind. Theoretical studies have investigated their generation mechanisms based on the 1D or 2D geometry of the structure. However, the generation mechanism is still unclear. Here we report on the 3D geometry of the electron-scale magnetic hole in the solar wind based on the Magnetospheric Multiscale mission. We find that the cross section of the magnetic hole with a size of ∼0.2–0.6 ρ i (ion gyroradius) is either circular or 2D sheet-like. Electron vortices exist in both kinds of cross sections. The ellipse is a possible candidate for the geometry of the magnetic hole in the plane including its axis. Surprisingly, such an elliptical geometry suggests that the axial lengths of all our selected magnetic holes are ∼1–2 ρ i . This 3D geometry might shed some light on the generation mechanism and role of the electron-scale magnetic hole in the astrophysical plasma.