A three-dimensional numerical model that coupled the arc, keyhole and weld pool was developed to investigate the keyhole behavior and energy transfer of an aluminum alloy in a variable polarity plasma arc welding process. The convective pattern in the weld pool was measured using an advanced x-ray transmission system. The elemental distribution of the bead was determined using an electron-probe microanalyzer. The coupled mechanisms of the keyhole, energy transfer, and compositional change were revealed. With a keyhole, both the arc energy loss and energy input increase, while the total energy transported from the arc to the weld pool decreases a bit, so the arc energy efficiency decreases. The heat flux at the keyhole is low and decentralized, resulting in low keyhole temperature; thus, the loss of elements with low boiling points due to evaporation can be ignored. Elements can be sufficiently mixed and distributed uniformly throughout the bead.