DRFNN is used to predict the evaporation state of wastewater, and incremental PID algorithm is combined to adjust the control quantity. By real-time monitoring the state and parameter changes of wastewater evaporation treatment process, online adjusting and optimizing the parameters of DRFNN and incremental PID, the automatic control of desulfurization wastewater evaporation treatment is completed. The experimental results show that this method can achieve more accurate and reliable automatic control, short control time, strong ability to deal with emergencies, and can converge to stability in a short time. This method can effectively reduce the number of early alarms and failures of the system and save maintenance costs. The IAE values of chloride ion (Cl) and mercury (Hg) in this method are 0.3558 and 0.3872, respectively, which proves that the difference between the actual output and the expected output of this method is very small, which proves that the system in this paper has high accuracy.