Abstract: The test data of the two phase flow instability contain some noise signal. When judging the unstable boundary of two-phase flow, the traditional method based on flow fluctuation amplitude has some limitations. In this paper, a method of FFT (fast Fourier transformation) based on pulsating was studied. The stable boundary was determined by capturing the characteristic signal on the frequency domain when the density wave instability occurred. The two sets of test data with different working conditions were analyzed. The results show that the present method has good accuracy.