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The temperature control ofcell incubator has some characteristics,for example,varing nonlinearity, time-lag, strongly coupling and difficult to establish accurate mathematical model of the object,and the traditional PID control also has some faults in holding the steady of cell incubator rapidly. In this paper, temperature deviation and temperature deviation rate as input,incubator temperature as control, the self-tuning fuzzy PID algorithm is proposed, which can achieve the real-time on-line correction of PID parameters.Experimental results show that the system stabilized the temperature within 37℃in 2890 seconds when it rose from 26℃ to 37℃.The stabilized temperature overshoot range in little areaand the temperature accuracy can keep in±0.05℃,and it was demonstrated on another incubator .The temperature regulation results show that the control algorithm better than traditional PID control of fastresponse, littleovershoot,high precision, itcansatisfydemandsoftemperaturecontrolof cell incubator.