Currently, Ball Mill is most used coal grinding equipment of pulverizing system of thermal power plant in China. Because of this system is multivariable, strong-coupling and serious time-delay, and it also has nonlinear, time-varying and distributed parameter characteristics. It is naturally difficult to be effective for such kind system to use PID regulation law and design multi-variable system by single-loop. So try more intelligent control for this kind system. Immune Control has fast response and robustness, especially; the Two-cell Immune Control has integration and memory characteristics, and improve the system to better control effect. It is particularly suitable for solving practical engineering application problems with robustness, adaptability and requirements of dynamic performance. So this paper use Two-cell Immune Control for the Ball Mill Control System, and make a large number of simulation experiments about rated parameter, non-rated parameter and adding disturbance situation, it has made a good dynamic and static performance under various conditions. These results confirm the validity of the design of Ball Mill Control System base on Two-cell Immune Controller.