Power generation is an important part of air vehicle energy management when developing long-endurance and reusable hypersonic aircraft. In order to utilize an air turbine power generation system on board, fuel-based rotating cooling has been researched to cool the turbine’s rotor blades. For fuel-cooling air turbines, each blade corresponds to a separate cooling channel. All the separate cooling channels cross together and form a distributary cavity and a confluence cavity in the center of the disk. In order to determine the flow characteristics in the distributary and confluence cavities, computational fluid dynamics (CFD) simulations using the shear–stress–transport turbulence model were carried out under the conditions of different rotating speeds and different mass flow rates. The results showed great differences between non-rotating flow and rotating flow conditions in the distributary and confluence cavities. The flow in the distributary and confluence cavities has rotational velocity, with obvious layering distribution regularity. Moreover, a high-speed rotational flow surface is formed in the confluence cavity of the original structure, due to the combined functions of centrifugal force, inertia, and the Coriolis force. Great pressure loss occurs when fluid passes through the high-speed rotational flow surface. This pressure loss increases with the increase in rotating speed and mass flow rate. Finally, four structures were compared, and an optimal structure with a separated outlet channel was identified as the best structure to eliminate this great pressure loss.