We have isolated the effect of kinetic energy of depositing species from the effect of flux pulsing during pulsed-laser deposition (PLD) on surface morphology evolution of Ge(001) homoepitaxy at low temperature (100 °C). Using a dual molecular beam epitaxy (MBE) PLD chamber, we compare morphology evolution from three different growth methods under identical experimental conditions except for the differing nature of the depositing flux: (a) PLD with average kinetic energy 300 eV (PLD-KE); (b) PLD with suppressed kinetic energy comparable to thermal evaporation energy (PLD-TH); and (c) MBE. The thicknesses at which epitaxial breakdown occurs are ranked in the order PLD−KE>MBE>PLD−TH; additionally, the surface is smoother in PLD-KE than in MBE. The surface roughness of the films grown by PLD-TH cannot be compared due to the early epitaxial breakdown. These results demonstrate convincingly that kinetic energy is more important than flux pulsing in the enhancement of epitaxial growth, i.e., the reduction in roughness and the delay of epitaxial breakdown.