Pore defects are one of the most common defects in the aluminum alloy electron beam welding process. In this paper, research on the pore defects and related mechanisms of the electron beam welding of dissimilar aluminum alloys was carried out with 1060 and 2A12 aluminum alloys. Under the test conditions, the pore defects of the aluminum alloy joint were related to the penetration status, the porosity of the critically penetrated joint was low, and the porosity of the beam joint increased when it was slightly penetrated. When the welding speed changed from 300 mm/min to 1200 mm/min, the porosity in the critically penetrated joint first increased and then decreased. When the welding speed was set to 300 mm/min and the beam current was set to 26 mA, the porosity of the joints reached its minimum value at 0.23%. Based on the actual process of electron beam welding, a flow simulation model was established to study the aluminum alloy welding process. The stability of the keyhole was related to the electron beam energy density reaching the inner keyhole, so increasing the electron beam for the fully penetrated joints was advantageous for reducing the pore defects.