The processes that occur during the electron beam welding are very complex. The main problem of electron beam welding is obtaining a reproducible cross section of the weld. This place is subjected to rigorous quality control during the welding of thin-walled joints. In particular, it is required to solve the problem of the welded joint optimal formation on the electron beam input/output section. The development of the mathematical models for the electron beam input and output modes, their joint use as a justification for the choice of the latter modes will allow a reasonable approach to the seam optimal formation in the area under consideration. In the framework of this study, the concept of an electron beam input-output control system for a weld optimizing in the electron beam welding process is presented. Within the framework of this concept, it mathematical and algorithmic software have to be developed for electron beam welding of thin-walled aerospace structures in terms of the electron beam input/output. Such approach will improve the quality of formed integral joints, as well as reduce the complexity of setting up the technological process of electron beam welding. It has to be developed and verified the mathematical models of temperature distribution under various modes of an electron beam input and output, models for optimizing input and output modes of an electron beam, and a software system prototype using the obtained models.