A low pressure fuel pump control system of a GDI engine may include a low pressure fuel pump primarily pressurizing fuel supplied from a fuel tank, a high pressure fuel pump secondarily pressurizing fuel from the low pressure fuel pump, a low pressure fuel pump pressure sensor and a high pressure fuel pump pressure sensor detecting fuel pressure of the low pressure fuel pump and the high pressure fuel pump, and a fuel supply pressure controller setting a final target pressure of the low pressure fuel pump by correcting a reference pressure, wherein the reference pressure is corrected by a low pressure correcting pressure according to temperature of the low pressure fuel pump and a correction pressure.