The profile of the laser beam plays a significant role in determining the heat input on the deposition surface, further affecting the molten pool dynamics during laser-based directed energy deposition. The evolution of molten pool under two types of laser beam, super-Gaussian beam (SGB) and Gaussian beam (GB), was simulated using a three-dimensional numerical model. Two basic physical processes, the laser–powder interaction and the molten pool dynamics, were considered in the model. The deposition surface of the molten pool was calculated using the Arbitrary Lagrangian Eulerian moving mesh approach. Several dimensionless numbers were used to explain the underlying physical phenomena under different laser beams. Moreover, the solidification parameters were calculated using the thermal history at the solidification front. It is found that the peak temperature and liquid velocity in the molten pool under the SGB case were lower compared with those for the GB case. Dimensionless numbers analysis indicated that the fluid flow played a more pronounced role in heat transfer compared to conduction, especially in the GB case. The cooling rate was higher for the SGB case, indicating that the grain size could be finer compared with that for the GB case. Finally, the reliability of the numerical simulation was verified by comparing the computed and experimental clad geometry. The work provides a theoretical basis for understanding the thermal behavior and solidification characteristics under different laser input profile during directed energy deposition.