Aiming at the liquid output blockage of one tank in two parallel tanks of the filling system during a certain mission, the physical model of the system is established to avoid similar problems, and the main causes of the problem are found by analyzing and calculating of the hydrodynamic continuity equation and kinetic equation. Using FLUENT simulation software to conduct the numerical simulation and result analysis of the confluence area of the two tanks, the root cause of the blockage problem of the outflow of parallel tanks is verified, and the targeted measures are proposed.