The hypersonic flow past a controlled rudder mounted at a gap to the aircraft fuselage is numerically investigated by solving three-dimensional (3D) Reynolds-averaged Navier-Stokes equations. This paper aims to explain the mechanism of production of extreme thermal environment faced by a rudder shaft from the view of physics of flow in the mounting gap. Simulations are conducted at Mach number of 10, and the gap ratio h/delta varies from 0 to 1.42, where h denotes the gap height and delta represents the thickness of the incoming turbulent boundary layer. Topological theory is utilized to identify the separation types. The formation of vortices is traced by extracting volume streamlines in the 3D space. The results indicate that the types of 3D separation appear in the gap shifts from the coexistence of horseshoe-type and tornado-type separations to only horseshoe-type separation that persists with the increase of h/delta. It is found that high heat flux is generated by the high-momentum fluid transported toward the surface by the horseshoe vortices. The tornado-type vortex prevents the incoming flow from arriving at the rudder shaft, which avoids the generation of high heat flux at the center of the rudder shaft. The rate of local heat transfer increases with h/delta as a result of the shrink and disappearance of the tornado-type vortices, which means that the region of low-speed backflow in front of the rudder is reduced and vanished. This study contributes to a clearer understanding of the flow physics in the complex disturbance area. (C) 2022 Author(s).