Aiming at the problem that Current Transformer (CT) affects differential protection, this paper proposes a new method to identify CT saturation based on Empirical Mode Decomposition (EMD). Differential current can be decomposed into few Intrinsic Mode Functions (IMFs) by EMD. When CT is linear transfer, the current waveform is nearly a sine wave, and it only contains one dominant IMF. However, CT saturation leads to the distortion of secondary current which contains at least two dominant IMFs. From the defined projection area on t-axis of each IMF and the specific gravity coefficient, the number of dominant IMF can be got. Thus CT saturation can be identified. Theoretical analysis and simulation results show that this method can identify CT saturation of different degree. It is convenient to achieve and hardly to be affect by aperiodic component.