For a high-speed vehicle in the presence of cavitating flow while operating near the free surface, the interaction between the cavitating flow and the free surface can be very critical. In this paper, the cloud cavitating flow over a Clark Y foil near the free surface was investigated via numerical approaches. The large eddy simulation (LES) turbulence model, the volume of fluid (VOF) method, as well as the Schnerr Sauer cavitation model were used in the simulation to solve for the cloud cavitation flow region and capture the interphase between the multiphase (air, water and vapour). The analysis centred on the results of the two- (2D) and three-dimensional (3D) cases for the Clark Y foil at various submerged depths for several evolution cycles. The free surface affects the cavity profile, evolution period, re-entrant jet inside/beneath the cavity and hydrodynamic coefficients. The cavity has become shorter and thicker under the free surface effect. Induced by the re-entrant jet thickness, the cavity becomes more stable as the submerged depth decreases. The cavity evolution, the cavity length and thickness of different cycles are similar, while the shedding cavity can delay the evolution. A similar phenomenon can be observed in 3D, but the flow structure is more complex than in 2D. The 3D effect likewise manifests as shortening the cavity length while changing the direction of the re-entrant jet inside/beneath the cavity.