To effectively improve weld forming and inhibit forming defects, taking 12 mm-thick 7N01 aluminum alloy as research object, the keyhole drilling process as well as the heat and fluid transport phenomena of electron beam spot welding (EBSW) were analyzed by Ansys Fluent and validated by experiments. In order to reflect the beam energy density distribution, a self-adaptive heat source model considering the characteristics of the active zone of beam was established, and VOF algorithm was used to track the gas-liquid interface in real time. Numerical analysis results show that the beam energy density distribution and the coupling between the beam and the transient pool/keyhole were the key factors to determine weld forming. When the beam was in lower focus mode, the unique energy distribution and the induced plasma insulation, metal vapor recoil pressure, Marangoni flow, and upward transportations of thermal buoyancy (maximum flow rate at about 15 m/s) led to the weld reinforcement and the extension of nailhead area. The beam energy density in the depth direction increased first and then decreased significantly, which resulted in similar evolutions for the welding in depth and width directions and might induce the spiking defects adjacent to the keyhole bottom. In addition, it was found that with the increase in keyhole depth, the energy fluctuation as well as the competition between recoil pressure and surface tension gradually increased, which promoted the periodicity of keyhole drilling process.