A new data processing method by means of Fourier transform has been developed. In Fourier transform, frequency leakage will surely be caused because of the space-limited extension of fringe pattern in Fourier transform. It will cause measurement error. The reason why frequency leakage is caused is analyzed, the corresponding numerical simulation is presented in detail, and the preliminary experiment is carried out. On the basis of the analysis, the numerical simulation and the experiment, it is proposed that external interpolation continuation of the fringe pattern to any integer times will greatly improve the measurement accuracy. The data processing method will promote the application of moiré deflectometry in micro-scale heat transfer and flow measurement.