For an incubation control system, which is multi-variable, strongly coupled, disturbed, and lagged largely, a hybrid intelligent control algorithm was proposed. The coupling of main parameters was decoupled by the former control, which used feed-forward decoupling algorithm. According to the difference of technological condition, the fuzzy-immune PID control algorithm or fuzzy control algorithm was selected subsequently. The temperature, humidity and oxygen content were controlled well by the hybrid intelligent control algorithm. The factual running results proved that the control algorithm of the incubation system is effective.