Uncertainty reduction is of great importance for laser-induced breakdown spectroscopy (LIBS). In this work, we modulated the evolution of the laser-induced plasma by shaping the laser beam from a commonly used Gaussian profile to a flat-top profile. With a more homogeneous distribution of laser power density, the flat-top beam was expected to achieve a more stable plasma morphology by more uniform ablation, which would lead to higher repeatability of LIBS signals, and to reduce plasma shielding effects by avoiding excessively high laser power at the center of the laser beam, which would lead to stronger signals. The results showed that by using a flat-top beam, the aluminum–magnesium alloy plasma morphology was meliorated with a larger and more stable plasma core, the relative standard deviation (RSD) of the Mg(I) 285.21 nm line was reduced from 33% to 18% for a laser energy of 30 mJ, and the signal intensity was enhanced 1.5 to 3.5 times for different laser energies. Overall, plasma modulation using beam shaping was proved to be very effective in improving LIBS signal quality.