This paper describes the heat transfer model of the compact heat exchanger in three levels. Heat transfer behavior of heat exchangers in air cycle refrigeration system is analyzed in two-wheel bootstrap air cycle system with low pressure water extraction system or with high pressure water extraction system. The agreement between the calculated results and the experimental data was very good. The results show that the behavior of compact heat exchanger under different conditions can be obtained with less experimental data. The approach can meet the requirements of engineering calculations and also provide a theoretical basis to evaluate the heat exchanger.