An operating system of a liquefied natural gas ship for performing sub-cooled liquefaction of boil-off gas includes a boil-off gas compressor, a cryogenic heat exchanger connected to a refrigerator system, and a first check valve and a first pressure control valve, installed in a pipe between a liquefied natural gas phase separator and a gas combustion unit, and a second check valve and a second pressure control valve, installed in a parallel pipe connected to the pipe in parallel. The parallel pipe is connected to a pipe between the boil-off gas compressor and the cryogenic heat exchanger such that boil-off gas is supplied to an upper vapor region of the liquefied natural gas phase separator. Thus, pressure and level of the liquefied natural gas phase separator are stably controlled. Power consumption is effectively reduced, and economical efficiency is achieved by stable operating pressure and level of the liquefied natural gas phase separator.