Based on the experiments of fiber laser beam welding 6061 aluminum alloy with 2.5 mm thickness, the effects of heat input on full penetration weld appearance are investigated. The results show that the weld width of the penetration weld increases with increasing the heat input, and the change amplitude of the weld back is greater than that of the weld front. When the stable fully penetration weld is used, a higher laser power results in a broader adjustable range of the heat input. Fine columnar microstructure is formed near the fusion zone, and the mixed microstructures (including columnar grains and equiaxed grains) is distributed in the center of the weld. When the heat input is reduced, the microstructures of the weld zone tend to fine, and the proportion of the equiaxed grains in the mixed microstructures decreases. In addition, with the heat input decreasing, the microhardness of the weld zone increases slightly, and the microhardness data dispersity between the weld up and weld bottom decreases. When the heat input is about 90 J/mm, the microhardness symmetry of weld up and weld bottom is best.