Three-dimensional shock/boundary layer interactions (SBLIs) in the hypersonic inlet generate the separation vortex, which affects the flow uniformity of the inlet and can even cause the inlet to unstart. This study experimentally investigates the separation vortex produced by a crossing SBLI in a supersonic quiet wind tunnel. Using a nanoparticle-based planar laser scattering method, the tomography-like three-dimensional structures of the separation vortex on the transverse, streamwise, and horizontal planes are demonstrated. The semi-elliptical separation vortex is formed from a pair of anti-rotating vortices and exhibits eddies around the vortex core; it remains stable in the absence of the expansion effect. Additionally, fractal dimension analysis reveals that the separation vortex core experiences stable streamwise development, while its outer edge is fragmented and dissipated due to the shearing effect of the mainstream. This investigation provides valuable insight for potential flow control to mitigate separation issues in hypersonic inlets.