The purpose of this paper is to find an equation of motion in a reasonable combination describing the manoeuvring motions in horizontal plane, rolling motion in lateral plane and seakeeping motion in vertical plane. The reasonable combination here is to find such a coordinates system as using the formulae with respect to the hydrodynamic forces which have been developed in field of manoeuvrability, stability and seakeeping. A new coordinate system called Horizontal Body Axes is presented for describing the equations of manoeuvring motion of a ship in waves. Froude-Krylov forces and Hydrodynamic forces on a ship are evaluated with respect to Horizontal Body Axes. The Time domain simulations are carried out for turning and zig-zag trial of a ship in waves. Finally, it is concluded that this new coordinate system would be considered to be available for describing ship motions having six degrees of freedom.