Extrusion through the porthole die is a predominant forming process used in the production of hollow aluminum alloy profiles across the aluminum extrusion industry. Longitudinal weld seams formed during the process may negatively influence the quality of extruded profiles. It is therefore of great importance to understand the formation of weld seams inside the welding chamber during extrusion, as affected by extrusion process variables and die design. Previously developed physical simulation methods could not fully reproduce the thermomechanical conditions inside the welding chamber of porthole die. In this research, a novel physical simulation method for the investigation of weld seam formation during extrusion was developed. With a tailor-designed tooling set mounted on a universal testing machine, the effects of temperature, speed, and strain on the weld seam quality of the 6063 alloy were investigated. The strains inside the welding chamber were found to be of paramount importance for the bonding of metal streams, accompanied by microstructural changes, i.e., recovery or recrystallization, depending on the local deformation condition. The method was shown to be able to provide guidelines for the design of porthole dies and choice of extrusion process variables, thereby reducing the scrap rate of aluminum extrusion operation.