Supercritical water reactor (SCWR) is one of generation IV nuclear reactors recommended by Generation IV International Forum (GIF). Compared to traditional pressurized water reactor (PWR), SCWR has a lot of advantages and it is the most promising one among the six kinds of generation IV nuclear reactors. However there is a sharp change of water properties in the core of SCWR, especially the change of water density which could result in potential flow instability, consequently the safety operation of SCWR will be threatened. Therefore it is necessary to carry out relevant investigation in this field.In this paper, a three dimensional (3D) numerical simulation is carried out using the CFX code to investigate the out of phase oscillation between two heated parallel channels with supercritical water. The numerical procedure is discussed and proper numerical models such as mesh number, coupling method between velocity and pressure, time step, difference scheme and turbulence model are selected. Then, instability boundaries are obtained under different inlet mass flow rates, system pressures, with and without gravity conditions. Because different physical models are adopted in the 3D simulation, the instability boundaries differ from those obtained with a 1D code. Finally, the numerical result is compared with experiment data, which shows that the 3D code could predict the onset of flow instability better than the 1D code. However there should be a further improvement of the physical models in the 3D code due to its inadequacy to predict the period of oscillation.