The invention relates to a preparation method of a sealed surface-mounted EMI filter and a welding tool thereof. The welding tool for preparing the sealed surface-mounted EMI filter comprises a bottomlayer supporting plate, a middle layer supporting plate and a top layer supporting plate, wherein a groove for accommodating a substrate is formed in the bottom layer supporting plate, the middle layer supporting plate is detachably connected with the bottom layer supporting plate, a through hole matched with the enclosure frame is formed in the middle layer supporting plate , when the middle layer supporting plate is connected with the bottom layer supporting plate, the through hole corresponds to the groove, the top layer supporting plate is detachably connected with the bottom layer supporting plate, and the top layer supporting plate is used for pressing and fixing the enclosure frame. The EMI filter is manufactured by means of the welding tool, thereby guaranteeing that the enclosureframe is just placed in the middle of a corresponding bonding pad on the substrate in the welding process, and avoiding the situation that the quality and attractiveness of a weld joint are affecteddue to horizontal deviation or inclined deviation; meanwhile, pressure is applied to the enclosure frame through using the top layer supporting plate, and the enclosure frame and the LTCC substrate are pressed tightly, thereby being conductive to exhausting gas in a weld joint during welding, guaranteeing that the weld joint is dense and free of pores and satisfying the air tightness requirement of a finished product.