Aiming at the problem of temperature tracking and balance control of each branch pipe of the heating furnace, an improved genetic algorithm was proposed to optimize the multi?deviation control of the temperature tracking and balance of the branch pipe temperature of the heating furnace. The scheme used the temperature deviation of the raw materials of each branch pipe after mixing and the temperature deviation of each branch pipe. By adjusting the feed flow rate and fuel flow rate, it not only ensured that the flow rate of the main pipe is constant during the regulation process, but also realized the dual goal of temperature tracking and balance of each pass. Multi?passes are analyzed as a whole, so the temperature comparison of adjacent branch pipes was avoided repeatedly. At the same time, the improved genetic algorithm was used to optimize the controller parameters of the differences control technique, which overcomes the difficulty of controller parameter tuning. The simulation results show the feasibility and effectiveness of the improved genetic algorithm to optimize the differences control scheme.