The design process of the combined thruster needs to consider the mutual influence between the stator, rotor and nozzle. Due to its complex structure, the influence of each component is ultimately reflected in the rotor-stator channel flow, resulting in intense internal flow and complex vortex structure in blade junction. In this paper, a LES simulation of the flow field inside the combined thruster is carried out to describe the vortex structure of the blade junction flow inside the rotor-stator channel using the Liutex method, focusing on the flow topology, and analyzing the effect of the junction flow at the stator hub on the development of the rotor root and tip vortex. The results show that the vortex structure of the rotor junction includes the horseshoe vortex, trailing vortex of the stator, the shedding vortex in the suction surface, and the tip vortex, which is caused by the boundary layer interaction in junction flow, the periodicity of the pre-stated stator, and the presence of the adverse pressure gradient in nozzle inner surface. The vortex system has an obvious periodicity. By identifying and analyzing the vortex structures of the junction flow, the influencing effects between the various components can be further understood, and guidance can be provided to reduce the vortex losses and improve the propulsion efficiency.