The invention discloses a filling type bobbin tool friction stir welding tool. The filling type bobbin tool friction stir welding tool comprises a stirring needle, a cavity shaft shoulder and a lower shaft shoulder; the cavity shaft shoulder is provided with a guide cavity; a filling rod is arranged in the guide cavity; a limiting boss for limiting shift-out of the filling rod is arranged at the lower end of the guide cavity; the filling rod is connected with a pushing system; one end of the pushing system is connected with a pressure plate mounted on the stirring needle, and the other end is positioned in the guide cavity; the cavity shaft shoulder is mounted on the stirring needle; and the lower shaft shoulder is mounted below the cavity shaft shoulder to form double shaft shoulders. According to the filling type bobbin tool friction stir welding tool, in high-speed rotating process of the stirring needle, one end, positioned at the lower end of the cavity shaft shoulder, of the filling rod is heated for softening, and is pushed to continuously enter a welding area by the pushing system to improve the welding quality; and as the filling rod is continuously extruded to enter the welding area by the pushing system, the defect of insufficient filling cannot be generated when welding is ended, the welding quality at the beginning of welding is consistent with the welding quality in the end of welding, and the joint welding strength is excellent.