Abstract: The cotton-gin automation is an important component in the cotton production process and also can affect cotton production quality, output, and profit etc. If keeping a constant seed cotton feed rate, a jam would appeared likely between the rotary knife and ribs of the cotton-gin stand when the moisture regain or seed cotton grade changed. In this paper, the automatic control system was designed that monitored and adjusted the seed cotton feed rate to produce a pre-selected load level on the cotton-gin stand rotary knife while automatically compensating for differences in the seed cotton such as trash and moisture regain content. In this automatic control system, an electrical transducer that is part of the automatic control system measured the input signal from a motor driving the rotary knife, and then proportionately converted and sent this signal as a direct current to the PLC by the AD module. Then the PLC sent the numerical signal to the upper computer. The intelligent controller in upper computer output the signal to the frequency changer that operated the rotational speed of feeding-cotton-rollers when the load changed on the cotton-gin stand rotary knife. According to the ginning characteristic, the adaptive fuzzy immune PID controller had been designed as the intelligent controller. And it was used to control the rotational speed of feeding-cotton-rollers with the purpose of suitable seed cotton feed rate. It was composed of the fuzzy controller, immune controller, and the traditional PID controller, and attempted to keep the system stable by adjusting the PID parameter in real time. So in this paper, three intelligent controllers (adaptive fuzzy PID controller, immune fuzzy controller, and adaptive fuzzy immune PID controller) were designed and analyzed respectively to compare the advantages and disadvantages of the three controllers. The modeling and simulation analysis in the Matlab were carried on, as well as the operational data was analyzed in actually using the process of the cotton-gin stand. The simulation results showed that the adaptive fuzzy immune PID controller was effective, feasible, and was superior to the other two intelligent controllers in stability, robustness, and especially in system response. The results of analyzing the operational data showed that the adaptive fuzzy immune PID controller could properly control the seed cotton feed rate to keep the cotton-gin stand working continuously without jam. In sum, by the use of the automatic control system with the adaptive fuzzy immune PID controller, the seed cotton feed rate could be controlled in real time to keep a suitable seed-cotton-roll density for the cotton-gin automation objective, when the moisture regain and seed cotton grade changed.