Abstract: Objective The aim was to solve the problems of forming and penetration control of dissimilar aluminum alloy complex welds in liquid cooling structures of aviation electronic equipment. Methods This paper systematically investigated influence of electron beam welding parameters on joint quality of 6061/5A06 dissimilar aluminum alloys. Through optimization of welding parameters and dynamic collaborative control technology of scanning and beam current, precision penetration welding of long welds, small curvature radius structures, and variable cross-section structures was achieved. Results The results indicated that scanning process effectively eliminated spike defects in aluminum alloy welding and optimized molten pool flow and energy distribution. By employing a scanning frequency of 200～500 Hz combined with an amplitude of 0.5～1.0 mm, penetration fluctuation was controlled within 0.2 mm. Conclusion Through dynamic collaborative regulation of beam current and focusing current, welding of complex paths and variable cross-section structures was accomplished, with penetration fluctuations controlled within 0.5 mm and 0.2 mm, respectively. The weld appearance, internal quality, and penetration depth all satisfied product requirements.