Electromagnetic vortex flowmeter is a new type of instrument for detecting leakage of steam generator, and the signal processing method based on the envelope to calculate energy ratio can effectively detect bubbles in sodium flow. The signal processing method is not affected by changes in the amplitude of the sensor output signal, which is caused by changes in magnetic field strength and other factors. However, the detection sensitivity of the electromagnetic vortex flowmeter is reduced. To this end, a signal processing method based on inverse Fourier transform to calculate energy ratio is proposed. According to the difference between the frequency band of the bubble noise signal and the flow signal, only the amplitude in the frequency band of the flow signal is retained in the frequency domain, and then the flow signal is obtained by the inverse Fourier transform method, thereby calculating the energy ratio. Using this method to process the experimental data, the results show that it can detect 0.1 g/s leak rate of water in the steam generator, and its performance is significantly better than that of the signal processing method based on the envelope to calculate energy ratio.