The present application discloses a method for performing a hole-plugging process on a circuit board. The method comprises: forming at least two locating holes on the circuit board; delivering the circuit board to a locating area of a hole-plugging screen printer, and adjusting a moving path of the circuit board in the locating area according to a locating device of the hole-plugging screen printer and the locating holes; and transporting the circuit board to a screen printing area of the hole plugging screen printer automatically according to the moving path, and adjusting a hole-plugging stencil of the hole-plugging screen printer to align an inking point of the hole-plugging stencil with a hole to be plugged on the circuit board, so as to plug ink dropped from the inking point of the hole-plugging stencil into the hole. The present application discloses a system for executing above method.