Nanosecond pulsed laser processing is a promising method to modify the microstructure of amorphous alloy. However, the heat and mass transfer mechanisms during processing are still unclear, which prevent regulating the microstructure precisely. In this study, a 3D heat transfer and flow coupling model is established to investigate the heat transfer and fluid flow behaviors, and their effects on the surface morphology and microstructure formation during the nanosecond pulsed laser processing of Fe78Si9B13 amorphous alloy. The physical processes such as melting and solidification, melt evaporation, melt convection and heat conduction, as well as the main driving forces such as surface tension, recoil pressure and gravity are taken into account in this model. The simulation morphology is in good agreement with the experimental results, indicating the validity of this numerical model. Based on simulation data analysis, it is found that the evolution mechanism of surface morphology is mainly related to the recoil pressure caused by evaporation and the Marangoni effect induced by the surface tension spatial gradient. Combined the temperature field analysis with experimental characterization, the formation mechanism of new amorphous phase in the molten zone (cooling rate at the order of 107 K/s) and the precipitation behavior of α-Fe(Si)/Fe-B phase nanocrystals in the heat-affected zone are clarified.