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High-precision thermal resistances are very often used in the sonic nozzle airflow standard facilities. In order to obtain the true transient temperature and minimize temperature effects on flow uncertainty, a thermodynamic model for flow temperature phenomena was presented and compared with experimental measurements. Numerical simulations using the software of FLUENT were carried out to analyze the difference between the experimental measurements and the model results. The analysis showed that such difference came from the temperature distribution in the stagnation tank. In addition, such difference could be ignored. In order to reduce the measurement uncertainty, a dynamic temperature compensation, which solved the actual model of thermal resistances and parameters of inverse model by least squares estimation method and wavelet filtering algorithm, had been presented. Comparing the output of the compensator with the true transient temperature obtained by the thermodynamic model, it proved the accuracy and the effectiveness of this compensation method.