This paper develops a numerical model to simulate the temperature field, residual stress and strain on an electron beam welding structure of 6061 aluminum, with the final aim of controlling welding distortion. The structure of the actual workpiece is very large and complicated, with the dimension up to 1000mm*300mm*20 mm, and there are totally more than 10 meters long welding lines on it. Different from establishing a partial simplified model to asses the characteristics of the whole workpiece, an integral three-dimension finite element model was built. Further, a much fine mesh was necessary to describe the heat source as the result of the high heat flow within less than 0.3mm diameter focus of electron beam, which will substantially enlarge the model in 3-dimension. A special finite element technique called local adaptive meshing was applied in this study, which can refine the mesh near the zone of heat source and recover it to its original density after heat source passes, thus reduce over 80 percent elements in the model. At the same time, a cluster composing of four PCs was built to carry out parallel calculation to further improve the calculation speed and quality of simulation. Using a thermal elastic-plastic analysis method, several welding processing parameters were systematically studied, as well as the influence of anti-form and milling after welding on the ultimate distortion. The results show that the welding parameters including heat input, welding speed and cooling condition have a direct effect on the welding temperature field, especially on the shape and dimension of the welding pool, which seriously influence the final residual stress, strain and distortion. Anti-form and milling also have effect on distortion, but not apparently as parameters mentioned above.