Spray Drying Absorber (SDA) has been widely used for large-scale desulfurization. However, it also has some limitations. For example, the liquid absorbent easily causes scaling, which impedes the contact between the serous fluid and the flue gas and reduces the chemical reaction rate and desulfurization efficiency. This paper establishes the mathematical and physical model of gas and liquid two-phase flow and droplet evaporation and heat transfer in rotary spray desulfurization tower. To study the accumulation and distribution of chemical reaction precipitates in the desulfurization tower and analyze the removal efficiency of sulfur dioxide (SO2) in different atomization diameters, this paper establishes a simulation model concerning the coupling of desulfurization reaction and flow field calculation based on the absorption and reaction mechanism of SO2. Baffle in different widths are set to optimize the internal flow field and balance the distribution of flue gas. By setting baffles of different widths to optimize the flow field in the tower and changing the distribution of flue gas, this model reduces the scaling while ensuring the desulfurization efficiency. The results of the simulation experiment have verified that the droplet with a diameter of 50 μm is the optimal option, which can effectively remove the scaling and ensure that the desulfurizing tower runs in high efficiency and stability. When the width of baffles is 2250 mm, the efficiency of desulfurization exceeds 95%, and the amount of scaling on the desulfurization tower main wall is controlled at the minimum level, which is the optimal option for production.