This paper is conced with the waves generated by a 3-D body advancing beneath the free surface with constant speed in a two-layer fluid of finite depth. By applying Green’s theorem, a layered integral equation system based on the Rankine source for the perturbed velocity potential generated by the moving body was derived with the potential flow theory. A four-node isoparametric element method was used to treat with the solution of the layered integral equation system. The surface and interface waves generated by a moving ball were calculated numerically. The results were compared with the analytical results for a moving source with constant velocity.