The invention discloses an electron beam welding method of a gas turbine casing with a horizontal flange structure, and relates to the welding method of the casing with horizontal flanges. The invention aims at solving the technical problems of large deformation, complicated tooling design and manufacture, low repetition usage rate of the tooling and low production efficiency after the horizontal flanges are welded by the existing half-ring gas turbine casing welding method. The welding method comprises the following steps of: 1, machining; 2, cleaning the surfaces of parts to be welded; 3, spot welding; 4, scribing; 5, assembling; 6, spot welding at fixed positions; 7, centering; 8, interpolating, and 9, welding the electron beam. Once vacuum electron beam welding of four horizontal flanges is achieved by the welding method disclosed by the invention; the deformation after welding is small; the production efficiency is doubled; X-ray flaw detection non-destructive testing is carried out; a welding line does not generate the defects such as lack of penetration, air holes, cracks and puncture; the quality of the welding line meets the requirements; and the electron beam welding method is simple in tooling design and manufacture, and high in repetition usage rate of the tooling, and can be used for welding the horizontal flanges of the gas turbine casing.