To obtain a better joint quality in butt welding of aluminum, the gap filling process and the quantification of the gap effects on the molten pool characteristic and the bubble formation were realized by a three-dimensional thermal-mechanistic-fluid coupled model, with the consideration of heat transfer, fluid flow, phase change and recoil pressure. The model was validated by the synchrotron-radiation result. The competition between the solidification and melting at the bottom of the molten pool was uncovered to determine the gap filling process and the molten pool morphology. Gap increased the heat loss, and the molten pool tip was elongated due to gap filling. Four phenomena appeared in sequence in the initial stage of butt welding: I. Gap filling; II. Frozen; III. Remelt; IV. Bubble formation. The result also demonstrated that the gap would disturb the molten pool. In the initial stable growth stage of the molten pool, the larger the gap width, the greater the molten pool depth. The sharp change of keyhole depth was due to the necking formation, while the small fluctuation of keyhole depth with larger gap values resulted from the perturbation by the gap. Bubble formation depends on the degree of the fluid flow and the gap filling due to the unique fluid dropping down phenomenon of butt welding with gap. A continuous melt pool cannot be formed when the gap width beyond 20 μm, which is detrimental to the welding quality. These findings are of great significance for guiding the optimization of butt-welding process, such as reducing the roughness of the butt interface or increasing the clamping force to reduce the butt gap.