The fuel filling system of a fuel pump reservoir includes: a reservoir mounted in a fuel tank; a fuel pump mounted in the reservoir and configured to deliver the fuel in the reservoir to an engine and to discharge a portion of the fuel to a fuel branch line; a relief valve disposed on a fuel supply line and configured to release pressure applied to the fuel supply line; a first jet pump configured to fill the reservoir with the fuel using fuel jet flow from the fuel branch line; a second jet pump configured to fill the reservoir with the fuel using fuel jet flow from a fuel return line; and a fuel pump control module (FPCM) configured to control operation of the second jet pump based on a driving mode of a vehicle.