A method and a system for determining a safe under keel clearance of an ultra-large ship are provided. The method comprises: acquiring operation parameter values of the ship; obtaining fluid pressure according to the values; obtaining a squat force and a trim moment of the ship according to the pressure; establishing a mirror image model based on speed potential to establish a squat clearance calculation model for the ship; determining a half-wave rising height with above calculation model; obtaining draught and trim changes according to the squat force and the trim moment, to determine a maximum squat clearance of the hull; determining the safe under keel clearance; and controlling the squat clearance of the ship according to the safe under keel clearance of the ship, to avoid navigation dangers, and improve the loading rate.