Abstract: Based on incubation control system which is multi-variable, strongly coupled and disturbed, lag largely, a fuzzy-immune Proportional-Integral-Derivative(PID) control method with hierarchical structure was presented. First, the coupling of main parameters was decoupled by the former structure which uses feed-forward decoupling algorithm, then fuzzy-immune PID control algorithm was proposed according to the characteristics of the surge and beyond enactment for the latter structure control, in which the main parameters including k_p,k_i, and k_d were adjusted according to fuzzy rules and nonlinear function was adjusted according to immune correction. Then, the parameters of PID were tuned by using immune regulation mechanism, thus, temperature, humidity and oxygen content in the incubation and hatching process were intelligently controlled. Finally, the running of system verified the effectiveness of the control algorithm.