The invention discloses a filing device of a three-dimensional package vertical through hole. The filling device comprises a metal liquid spraying device and a filling working region and is characterized in that a crucible is of an internally-externally nested circular ring type structure, a cavity between an internal accommodating cavity and an external accommodating cavity is filled with a filling material, a press sheet is driven by a transmission rod connected with piezoelectric ceramic to squeeze a metal liquid in a central hole to be sprayed from a spraying hole, the crucible is connected with the upper part of the cavity by a crucible support connected with a three-dimensional motion controller, so that the crucible moves freely and is matched with a substrate of the filling working region to complete filling. The invention also discloses a method applying the above device for filling the three-dimensional package vertical through hole. With coordination of the metal liquid spraying device and a working platform of the filling working region, uniform liquid drops can be formed, the frequency is controllable, a steady-flow liquid line also can be formed, and metallic filing of the three-dimensional package vertical through hole is achieved. The filling device has the advantages of high size accuracy, low porosity, high filling efficiency, low cost and simplicity in process, and can be automatically produced.