Polymer–metal hybrid structures combine the merits of polymer and metal materials, making them widely applicable in fields such as aerospace and automotive industries. However, the main challenge lies in achieving efficient and strong connections between the metal and polymer components. This paper uses the jet electrochemical machining (Jet-ECM) method to customize the surface morphologies on 6061 aluminum alloy (AA6061) sheets. The connection between AA6061 and carbon fiber-reinforced PA66 (CF/PA66) is then achieved through hot pressure welding (HPW). The effects of aluminum alloy surface morphology, welding force, and welding time on the mechanical properties and microstructure of the joint are investigated. The optimal process parameters are determined by the design of the experiment. The results show that the aluminum alloy surface morphology has the greatest impact on the mechanical property of the welded joint. The optimal process parameters are surface morphology with wider, shallower, and sparsely distributed grooves on the aluminum alloy surface, the welding force is 720 N, the welding time is 12 s, the welding temperature is 360 °C, the cooling time is 16 s, and the optimal peak load of the joint is 6690 N. Under the optimal parameters, the fracture morphology in the AA6061 side is almost entirely covered with CF/PA66. The joint experiences cohesive failure in most areas and fiber-matrix debonding in a small area.