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Thermoelectric cooler has dynamic thermoelectric performance under complex environment. A dynamic model of thermoelectric cooler is derived using small-signal linearization method. It shows that the dynamic model of the thermoelectric cooler has one zero and two poles. The dynamic model of thermoelectric cooler is shown to vary with different operating condition. Based on average linear dynamic model of a thermoelectric cooler, a temperature control system is designed for the cold end temperature of the thermoelectric cooler using adaptive NN-PID algorithm. The step response tests show that the controller has satisfying dynamic and steady performance. In room temperature environment, the response time for cooling down 10_ is around 70s and the steady error is very small. The cold-end temperature can be maintained at the setting value within 0.1_. Experiment results also show that the setting temperature can reach to 23_ below the environment temperature. The smaller setting value is, the longer step response is.