The controlled object of boiler combustion system in power plant is a complex system with nonlinear, timing change, large lagging and multi-variable coupling, and does not have precise mathematical model, so it is difficult to obtain the satisfactory control effect adopting the traditional PID control. Advanced control strategies are adopted to improve the performance of the boiler combustion control system, and it has been more and more the concern of the majority of electricity production enterprises. Internal model control is a very practical control method, and its main characteristic is simple structure, intuitive design and few online adjustment parameter, and easy adjustment policy. And it is especially particularly significant to improve the control effect of large delay system. The internal model control system is used in power station boiler combustion system, it can effectively solve the large delay, large inertia and other shortcomings, but there is the contradiction between the fast response and robustness in internal model control system. The fuzzy immune control has advantages, such as, fast response, fast stable and good robust, etc. The fuzzy immune control is introduced into internal model control system, this paper designs fuzzy immune internal model controller, which integrates speed and robustness of the internal model control. The fuzzy immune internal model control is applied to combustion control system, and we compare it with ordinary internal model control method. The simulation result shows that fuzzy immune internal model control can greatly improve the characteristics of the control system with time delay. And this effectiveness of the fuzzy immune internal model controller has been verified.