It is challenging to predict the morphology of the grooves ablated by pulsed laser. To predict the morphology and surface roughness of aluminum alloy grooves at low laser fluence (ranging from 17.68 J/cm2–28.29 J/cm2), a method which combines analytical and simulation approaches is proposed in this research. The proposed method takes into account the evaporation and redeposition behavior, examines the impact of pulse interactions through simulations, and focuses on the influence of molten pool flow on surface roughness. Firstly, the level set method is employed to accurately track the vapor-liquid interface and predict the ablative morphology of a single pulse. Secondly, the influence of molten pool flow on surface morphology in the case of pulse interaction is quantitatively described by comparing the morphology of a two-pulse ablation simulation with scanning speed in the heat source to the morphology obtained by simple superposition of a single pulse, the resulting morphological error is attributed to flow. Finally, the flow deviation of the ablated groove is compensated for applying an analytical method, and the three-dimensional morphology of the ablated groove is calculated by using the proposed expression. The computational analysis using the new method is compared with the experimental results, demonstrating that the average prediction error for contour is less than 7 %, and the error for roughness prediction is less than 10 %. By analyzing the melt flow using the new method, it is discovered that as the laser fluence increases, the range of melt flow expands and the amplitude of vertical flow increases, which results in the increase of surface roughness. Notably, the scanning speed does not directly affect the roughness by influencing the melt flow.