Abstract: In terms of physical transportation characteristics of 2024 aluminium alloy electron beam spot welding, on the basis of conservation equations of mass, momentum, energy and VOF (volume of fluid) equation, a 3D mathematical model for electron beam deep-penetration welding was established. By using this model, the evolutions of temperature field and keyhole for spot welding pool at the heating stage and the cooling backfilling stage were systematically described and validated by weld shape comparison. The results indicate that the vapour-induced recoil pressure is the key driving force for keyhole formation and deepening. As soon as the keyhole appears, the maximum temperature region of welding pool at the heating stage is located at the bottom of the transient keyhole. Meanwhile, the cooling rate of welding pool is increased from the upper to the bottom, which results in the grain refining of weld microstructure.