The invention discloses a method for welding a heterogenous system aluminum alloy through electron beams. Welding base metal is an aluminum-silicon cast aluminum alloy and an aluminum-magnesium wrought aluminum alloy. The method specifically includes the following steps of (1) joint designing, (2) preweld cleaning and assembling, (3) setting of welding parameters of the electron beams, (4) setting of injection positions of the electron beams, (5) welding, (6) modification welding and (7) postwelding cleaning. By means of the method, the welding quality is improved; the welding cost is reduced; meanwhile, the method is free of the special requirement for the environment and does not need special preweld and postwelding treatment; the welding process is easy to implement; the work efficiency is high; the method is quite wide in application prospect.