A two-way coupling Discrete Phase Model (DPM) is applied to calculate the secondary atomization process. The particle flight and cooling processes are studied under different process parameters. The results show that the average particle size (d50) depends on the gas-liquid interaction and decreases with increasing gas-to-melt ratio (GMR). The standard deviation of the particle size (d84/d50) increases as the melt mass flow rate increases, and both high and low atomization pressures result in a high d84/d50. The average cooling rate of particles can be improved by reducing the melt mass flow rate and increasing the atomization pressure. By increasing the gas temperature to 400 K, the d50 can be significantly reduced and the average cooling rate can be approximately increased two times, indicating that the hot gas atomization technique can effectively improve the yield of fine amorphous powders. However, excessive gas temperature not only has a limited effect on improving the cooling rate, but also significantly increases the d84/d50 and defective particles, suggesting that the gas temperature must be matched to the atomization process to achieve ideal effects. The powders produced at 2.0 MPa and 0.075 kg·s−1 exhibit good circularity with a d50 of 58.9 μm, which is in good agreement with the simulation analysis. Moreover, the powders with sizes less than 50 μm exhibit high amorphous fraction (96.6%) and outstanding soft magnetic properties. In this work, a flow-heat transfer-DPM coupling model is established to provide theoretical guidance for the production of high-performance Fe-based amorphous powders.