The method is based on that the waveform of the inrush distorts seriously, while the fault current nearly keeps sinusoid. The complicated signal can be decomposed into a finite intrinsic mode functions (IMF) by the EMD, then define and compute the projection area on X-axis of each IMF—, the specific gravity of SIMF—, and the maximum of —. We can get a new scheme of transformer-protection based on comparing the difference between inrush and fault current. Theoretical analysis show that the method can precisely discriminate inrush and fault current, fault clearance time is about 20ms. Moreover, it is convenient to achieve and hardly be affect by not-periodic component.