The invention relates to a container corrugated weld joint automatic welding tool and a welding method used by the same. The welding tool comprises a welding device, two transporting machines and a turnover device, wherein the welding device comprises a bottom beam, a welding platform which is arranged on the bottom beam and can slide in the length direction of the bottom beam in a reciprocating mode, and a welding robot arranged on the welding platform, the turnover device is arranged between the two transporting machines, and the turnover device comprises a turnover frame body, a turnover frame and a driving oil cylinder, wherein the turnover frame is arranged on the turnover frame body, one end of the turnover frame is rotationally connected with the turnover frame body, and the two ends of the driving oil cylinder are correspondingly and rotationally connected to the turnover frame body and the turnover frame. In the container corrugated weld joint automatic welding tool, the turnover device is used for realizing turnover of sectional materials, moreover, welding of the sectional materials subjected to turnover is realized by the aid of the welding device, the welded sectionalmaterials can be conveyed to a next station through the transporting machines, so that the automation of welding and the streamlined production are realized, and the production efficiency and the production quality are greatly improved.