Based on the kinetic equation and kinematic equation, trajectories of a new blended-wing-body(BWB) underwater glider are simulated with a changing deflection of the center of gravity (CG), which indicates that the glide ratio degrades with the deflection of the center of gravity going larger. Numerical study on the store separation from the weapon bay of a BWB underwater glider, supported by the computational fluid mechanics and the six-degree-of-freedom model, is carried out. The specified separating course and the flow structure of the weapon bay are demonstrated. With the calculated hydrodynamic forces, the kinetic equation and kinematic equation are solved to get the affected trajectories of different attack angles.