In hatching process, temperature, relative humidity and oxygen concentration are three main parameters to the success of the incubator. Incubation system is a multi-variable multi-interference and time delay complex dynamic system, a hybrid intelligent control method is proposed. Based on characteristics of complexity and uncertainty for its mathematical models in the hatching process, this paper will divide the system into two structures, considering of the effect of throttle opening which causes temperature and relative humidity big interference and strong coupling, feed-forward compensation decoupling control algorithm is employed for before-class structure to realize the decoupling of main parameters. After decupling, according to different conditions fuzzy immune PID control algorithm or fuzzy control algorithm is selected for back-class structure to realize incubator intelligent control. Finally, the run of system verifies the effectiveness of the control algorithm.