There are complex flows such as the shock-boundary layer interaction and the shock-leading edge vortex interaction in the highly swept flying-wing configuration at transonic speed, and the flows have serious effect on the flow and erodynamic characteristics. To compare the flow detail of the thin body model and the thick body model, the effect of the wing-body thickness on flow characteristics and the flow mechanism are analyzed by the simulation method. The results show that: At the small attack angle, there is a sidewash effect in the nose and shock-boundary layer interaction which leads to a flow separation in tail due to the quick tail contraction; at the middle attack angle, the sidewash effect of wing-body thickness makes the leading vortex appear later and the effect zone to be smaller, but it also makes the vortex strength and the wall suction increase, and the effects make the vortex lift change little. The shock in the middle model due to the wing-body thickness would pass through the leading edge vortex and induce the leading edge vortex breakdown, which makes the vortex breakdown angle and vortex lift to be reduced.