The invention discloses a device and a method for controlling a fuel supply system, and the device is applicable to a hydraulic free-piston engine, wherein, a piston position detection module is connected with a piston and a signal control module respectively for detecting the position of the piston and transmitting a position signal of the piston to the signal control module; the signal control module is connected with a drive module for processing the position signal of the piston and transmitting a corresponding control signal to the drive module; and the drive module is connected with an electromagnetic valve for outputting control current to complete the on/off of the electromagnetic valve. With the adoption of the technical proposal of the invention, the control of injection timing and fuel delivery can be accurately realized, and the closed-loop control can be performed to the fuel delivery to guarantee that the lower dead point of the piston of the hydraulic free-piston engine has an accurate position, so that the hydraulic free-piston engine can have a stable functional mode.