The motion response analysis of a submerged elliptic cylinder in waves is presented and the elliptic cylinder is a simplification of the section of submarine in this paper. The method is based on boundary integral method and two-dimensional 3 degree motions are calculated in regular harmonic waves. The fully nonlinear free surface boundary condition is assumed in an numerical domain and this solution is matched along an assumed boundary as a linear solution composed of transient Green function, The large amplitude motions of an elliptic cylinder are directly simulated and effects of wave frequency, wave amplitude and the distance from buoyancy center to gravity center are discussed.